Citrus tristeza virus based vectors for foreign gene/s expression

ABSTRACT

Disclosed herein are viral vectors based on modifications of the  Citrus  Tristeza virus useful for transfecting  citrus  trees for beneficial purposes. Included in the disclosure are viral vectors including one or more gene cassettes that encode heterologous polypeptides. The gene cassettes are positioned at desirable locations on the viral genome so as to enable expression while preserving functionality of the virus. Also disclosed are methods of transfecting plants and plants transfected with viral vector embodiments.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation-in-part of U.S. Ser. No. 13/624,294filed Sep. 21, 2012 and further claims the benefit of U.S. ProvisionalApplication No. 61/537,154 filed Sep. 21, 2011 and U.S. ProvisionalApplication No. 61/970,975 filed Mar. 27, 2014, all of which areincorporated herein by reference in their entirety.

BACKGROUND

The early development of viral vectors was aimed at the inexpensiveproduction of high levels of specialty proteins that could be scaled upin the field. The first attempt at a plant viral vector utilizedCauliflower mosaic virus, a dsDNA virus (Brisson et al., 1984;Gronenborn et al., 1981). However, this vector was too unstable to beuseful (Fütterer et al., 1990). The development of reverse geneticssystems amenable for manipulation of RNA viruses made many more virusescandidates for vector development (Ahlquist et al., 1984).

Virus vectors are key ingredients in basic research and have greatpotential for commercial applications. Lack of stability of foreigninserts has been a major drawback for potential applications of virusvectors for commercial protein expression in field applications.

SUMMARY

The present disclosure is based on multiple studies testing the vectorlimits of using CTV to express foreign genes ranging from 806 to 3480nucleotides in size. In one embodiment, gene cassettes were introducedinto the CTV genome as replacement of the p13 gene. In otherembodiments, a gene was inserted at different locations (e.g., p13-p20,p20-p23 and p23-3′NTR (non-translated region)). In another embodiment, afusion to p23 and protease processing were tested. In alternativeembodiments, genes were inserted behind IRES sequences to createbi-cistronic messages.

Twenty seven expression vectors have been created and tested inNicotinia benthamiana protoplasts and plants. Remarkably, most of thenewly developed vector constructs disclosed herein replicated, spreadsystemically in plants, and produced their foreign gene(s). The highestexpressing vectors tested include the “add a gene” constructs having aninsertion between the p13 and p20 genes or between the p23 gene and the3′NTR. Similarly, the vectors with the inserted gene replacing the p13gene effectively expressed different reporter genes. However, optimalexpression of the reporter gene depended both on the size and locationof the insertion. Optimal expression of smaller genes are from positionsnearer the 3′ terminus, whereas larger genes are optimally expressedfrom more internal positions.

Efficient expression of two genes simultaneously from the same vectorhas been accomplished in both N. benthamiana and citrus. The novel CTVconstructs disclosed herein have genomes with unique elasticity capableof accommodating and expressing foreign gene/s by different strategies.

Engineering an effective vector requires a balance between differentfactors. The vector needs to be designed such that replication andsystemic movement in the plant are reduced minimally while the level ofexpression of the foreign protein is maximal (Shivprasad et al., 1999).The final factor is the stability of the vector. In general, thevector's usefulness is directly correlated with its stability. Stabilityis a product of reduced recombination and increased competitiveness ofthe vector with the resulting recombinants that have lost part or all ofthe inserted sequences.

BRIEF DESCRIPTION OF DRAWINGS

FIG. 1. GFP replacement of p13 to produce CTV based expression vectors.(A) Schematic representation of CTV9RΔp33 (Boxes represent open readingframes with blue outline of boxes represent the replication gene blockwhereas the red outline represent the closterovirus conserved gene block(Karasev, 2000). The black circle and black boxes outline representsilencing suppressors (Lu et al., 2004). Gold box outline representgenes dispensible for the infection of some citrus genotypes (Tatineniet al., 2008). Filled black rectangle represents the deletion of the p33controller elements and ORF (nts 10858-11660 Genebank Accession #AY170468) (Satyanarayana et al., 1999; 2000; 2003)). Arrows indicate theprocessing of the leader proteases of CTV, LP1 and LP2 are two tandemleader protease, MT (methyl transferase), Hel (Helicase), RdRp (RNAdependent RNA polymerase, Δp33 (deletion of the 33 kda proteinsequence), p6 (6 kda protein), Hsp70h (heat shock protein 70 homologue),p61 (61 kda protein), CPm (minor coat protein), CP (major coat protein,inter cellular silencing suppressor), p18 (18 kda protein), p13 (13 kdaprotein), p20 (20 kda protein, inter/intra cellular silencingsuppressor), p23 (23 kda protein, intracellular silencing suppressor)and modification to produce expression vectors CTV33-Δ13-BY-GFP-57(C57), CTV33-Δ13-G-GFP-65 (C65), CTV33-Δ13-B-GFP-66 (C66) with the CP-CEof BYSV, GLRaV-2 and BYV driving GFP, respectively. (B) Northern blotanalysis of wild type CTV (WT) and CTV based expression vectortransfected to N. benthamiana protoplast (T) and passaged to a new setof protoplasts (P). (C) Representative sample of fluorescence in N.benthamiana infected with either of the three constructsCTV33-Δ13-BY-GFP-57, CTV33-Δ13-G-GFP-65, CTV33-Δ13-B-GFP-66 magnifiedunder a fluorescent stereoscope. (D) Representative sample offluorescence in the phloem of citrus bark pieces infected withconstructs CTV33-Δ13-G-GFP-65 and CTV33-Δ13-B-GFP-66 with high (left)and low (right) magnification under a fluorescent stereoscope.

FIG. 2 GUS replacement of p13 to produce CTV based expression vectors.(A) Schematic representation of CTV9RΔp33 and its modification creatingexpression vector CTV33-Δ13-BY-GUS-61 in which the p13 and itscontroller element is replaced by GUS under the control of CP-CE ofBYSV. (B) Northern blot hybridization analysis of wild type CTV (WT) andCTV based expression vector CTV33-Δ13-BY-GUS-61 (C61) transfected to N.benthamiana protoplast (T) and passaged to a new set of protoplasts (P).(C) Representative sample of GUS activity in the bark pieces of citrustrees infected with construct CTV33-Δ13-BY-GUS-61 (right) and the GUSsolution before fixing of the bark pieces (left) (A=Healthy control,B=infect).

FIG. 3 GFP insertion between p13 and p20 to produce CTV based expressionvectors. (A) Schematic representation of CTV9RΔp33 and modification byinserting between p13 and p20 of GFP ORF under the control of BYSVcreating expression vector CTV33-13-BY-GFP-69 (B) Northern blothybridization analysis of transfected protoplast with the wild typevirus (WT) and expression vector CTV33-13-BY-GFP-69 (C69) fromtranscripts (T) and their passages (P). Representative sample offluorescence in N. benthamiana (C) and peeled bark phloem pieces of C.macrophylla (D) infected with CTV33-13-BY-GFP-69 magnified under afluorescent stereoscope.

FIG. 4 GFP insertion between p20 and p23 to produce CTV based expressionvectors. (A) Schematic representation of CTV9RΔp33 and its modificationproducing expression vector CTV33-20-B-GFP-49 and CTV33-20-BY-GFP-58,respectively. (B) Northern blot hybridization analysis of transfectedprotoplast with the wild type virus (WT) and expression vectorsCTV33-20-B-GFP-49 (C49) and CTV33-20-BY-GFP-58 (C58) from transcripts(T) and their passages (P). (C) Flourescence under UV light ofprotoplast (right) and the leaf (left) showing lack of efficientmovement of the vector. (D) Western blot analysis of the same geneinserted at different locations in the CTV genome. BCN5 (Folimonov etal., 2007) original CTV vector (contains GFP under BYV promoter betweenCPm and CP), constructs CTV33-23-BY-GFP-37 (C37, insertion of BYSVdriving GFP behind p23), CTV33-20-BY-GFP-58 (C58, insertion of BYSVdriving GFP between p20 and p23), CTV33-13-BY-GFP-69 (C69, insertion ofBYSV driving GFP between p13 and p20), CTV33-Δ13-BY-GFP-57 (C57,replacement of p13 gene with BYSV CP-CE driving GFP) andCTV33-27-BY-GFP-63 (C63, Insertion of BYSV CP-CE driving GFP ORF betweenCPm and CP).

FIG. 5 GFP insertion between p23 and 3′NTR to produce CTV basedexpression vectors. (A) Schematic representation of CTV9RΔp33 and itsmodification by insertion of GFP behind p23 under control of CP-CE ofBYSV, GLRaV-2 and BYV creating expression CTV33-23-BY-GFP-37 (C37),CTV33-23-G-GFP-40 (C40) and CTV33-23-B-GFP-42 (C42), respectively. (B)Northern blot hybridization analysis of transfected protoplast with thewild type virus (WT) and expression vectors CTV33-23-BY-GFP-37,CTV33-23-G-GFP-40 and CTV33-23-B-GFP-42 from transcripts (T) and theirpassages (P). (C) Representative sample of fluorescence in N.benthamiana infected with either of the three constructsCTV33-23-BY-GFP-37, CTV33-23-G-GFP-40 and CTV33-23-B-GFP-42 magnifiedunder a fluorescent stereoscope. (D) Representative sample offluorescence in the phloem tissue of Citrus macropylla infected withconstructs CTV33-23-BY-GFP-37 and CTV33-23-G-GFP-40.

FIG. 6 GUS insertion between p23 and 3′NTR insertion between p23 and3′NTR to produce CTV based expression vectors. (A) Schematicrepresentation of CTV9RΔp33 and modification by insertion of GUS ORFunder control of BYSV CP-CE between p23 and 3′NTR creating expressionvector CTV33-23-BY-GUS-60 (C60). (B) Northern blot hybridizationanalysis of transfected protoplast with the wild type virus (WT) andexpression vectors CTV33-23-BY-GUS-60 from transcripts (T). (C)Enzymatic activity of the GUS protein in N. benthamiana tissue andcitrus phloem bark pieces (Blue color indicate infected plant andcolorless tissue and solution indicate healthy control and GUS solutionsubject to the same treatment.

FIG. 7 GFP inserted behind IRES sequences to create CTV based expressionvectors. (A) Schematic representation of CTV9RΔp33 and CTVΔCla 333R andtheir modification behind p23 creating expression vectorsCTV33-23-ITEV-GFP-41; CTV33-23-I3XARC-GFP-43 represent the TEV 5′NTRIRES and 3xARC-1 IRES, respectively and CTVp333R-23-ITEV-GFP;CTVp333R-23-I3XARC-GFP representing the TEV 5′NTR IRES and 3xARC-1 IRES,respectively. (B) 1-Northern blot hybridization analysis fromtransfected N. benthamiana protoplast with wild type virus (WT),CTV33-23-ITEV-GFP-41 (C41) and CTV33-23-I3XARC-GFP-43 (C43); T=RNAisolated from transcript transfected protoplast and P=RNA isolated fromvirion transfected protoplast isolated from RNA transfected protoplast.2-Northern blot hybridization analysis from protoplast transfected withCTVp333R-23-ITEV-GFP (Lane A); CTVp333R-23-I3XARC-GFP (lane B), CTVp333R(lane C) and CTVp333R-23-B-GFP (BYV CP-CE driving the expression of GFPbehind p23) (Lane D).

FIG. 8 GFP and a protease fused to p23 to create CTV based expressionvectors. (A) Schematic representation of CTV9RΔp33 and the modificationsby fusing two TEV proteases (NIa and HC-Pro) and their recognitionsequences to create expression vectors CTV33-23-HC-GFP-72,CTV33-23-NIa-GFP-73, CTV33-23-HCØ-GFP-74 and CTV33-23-NIaØ-GFP-75.

FIG. 9 Comparison of Florescence in N. benthamiana. (A) Comparison offlourescence in infiltrated leaves of representative samples ofconstructs CTV33-23-HC-GFP-72, CTV33-23-NIa-GFP-73, CTV33-23-HCØ-GFP-74and CTV33-23-NIaØ-GFP-75 (GFP fused) and CTV33-23-BY-GFP-37,CTV33-23-G-GFP-40 and CTV33-23-B-GFP-42 (free GFP) under hand held UVlight (Right) and the same leaves under white light (left). (B)Comparison on whole plant level between representative samples ofconstructs CTV33-23-HC-GFP-72 and CTV33-23-NIa-GFP-73 (fused GFP) andCTV33-23-BY-GFP-37, CTV33-23-G-GFP-40 and CTV33-23-B-GFP-42 (GFP underits own controller element behind p23 (Free GFP)) under hand held UVlight (Right) and same plants under white light (Left). (C) Comparisonbetween the abaxial (Lower) and adaxial (upper) leaf surfaces of thesame representative leaf sample of constructs CTV33-23-HC-GFP-72 andCTV33-23-NIa-GFP-73 under hand held UV light (Right) and white light(Left).

FIG. 10 Western blot analysis of different expression vectorsinfiltrated into N. benthamiana leaves using GFP antibody.A=CTV9RΔp33GFP (GFP inserted under the BYV CP-CE controller elementbetween CPm and CP (produces free GFP) (Tatineni et al., 2008)),B=CTV33-23-BY-GFP-HC-GUS-51, C=CTV33-23-G-GFP-NIa-GUS-54, D=Empty well;E=CTV33-Δ13-BY-GFP-NIa-GUS-78, F=CTV33-23-HC-GFP-72,G=CTV33-23-NIa-GFP-73.

FIG. 11 Hybrid gene (GFP/Protease/GUS fusion) replacement of p13 tocreate expression vectors. (A) Schematic representation of CTV9RΔp33 andits modification to create expression vectors CTV33-Δ13-BYGFP-HC-GUS-77and CTV33-Δ13-BYGFP-NIa-GUS-78 with the two fusion genes under thecontrol of BYSV CP-CE with TEV HC-Pro and NIa spanned by theirproteolysis recognition sequence separating GFP and GUS, respectively.(B) Activity of the reporter genes in N. benthamiana and Citrusmacrophylla. (a.) Representative sample of N. benthamiana plant infectedwith either CTV33-Δ13-BYGFP-HC-GUS-77 or CTV33-Δ13-BYGFP-NIa-GUS-78 N.benthamiana under white light and (b.) the same plant under UV light(c.) Two pictures of peeled phloem bark pieces of C. macrophyllainfected with construct CTV33-Δ13-BYGFP-NIa-GUS-78 under a fluorescentstereoscope (d.) Representative sample of GUS activity in systemic N.benthamiana leaves, control leaf (Left) and infected leaf (right) (e.)Peeled bark phloem pieces and GUS solution of healthy C. macrophyllaplant (f.) Peeled bark phloem pieces of C. macrophylla plant infectedwith construct CTV33-Δ13-BYGFP-NIa-GUS-78.

FIG. 12 Stability of Constructs in N. benthamiana. (A) Upper leaf fromAgro-inoculated N. benthamiana plants carrying the binary vectorCTV33-Δ13-BYGFP-HC-GUS-77 (GFP/HC-Pro/GUS) pictured under fluorescentmicroscope. (B) The same leaf was tested for GUS activity indicatingalmost perfect overlap between the two reporter genes.

FIG. 13 Hybrid gene (GFP/Protease/GUS fusion) between p23 and 3′NTR tocreate expression vectors. (A) Schematic representation of CTV9RΔp33 andits modification to produce expression vectors CTV33-23-BY-GFP-HC-GUS-51and CTV33-23-BY-GFP-NIa-GUS-52 has the BYSV CP-CE driving the hybridgenes that contain HC-Pro and NIa proteases respectively;CTV33-23-G-GFP-HC-GUS-53 (C53) and CTV33-23-G-GFP-NIa-GUS-54 (C54) areGLRaV-2 driven fusion genes that contain the HC-Pro and NIa proteases,respectively; CTV33-23-BY-GFP-HC-GUS-55 (C55) andCTV33-23-BY-GFP-NIa-GUS-56 (C56) are BYV driven fusion genes thatcontain HC-Pro and NIa proteases, respectively. (B) Northern blothybridization analysis of transfected protoplast with wild type virus(WT), C53, C54, C55 and C56 constructs.

FIG. 14 Activity of reporter genes generated by insertion of the Hybridgene (GFP/Protease/GUS fusion) behind p23. (A) Activity of the reportergenes in N. benthamiana. plants (a.) Representative sample of N.benthamiana plant infected with CTV33-23-BY-GFP-HC-GUS-51,CTV33-23-G-GFP-HC-GUS-53, CTV33-23-BY-GFP-NIa-GUS-52 orCTV33-23-G-GFP-NIa-GUS-54 under white light and (b.) the same plantunder hand held UV light (c.) Representative sample of GUS activity ininfected systemic N. benthamiana leaves and control leaves (tubes 1 &2represent the solution before fixing and tissues in fixing solution,respectively from healthy leaves whereas 3&4 represent the solution andtissues from infected leaves, respectively, G tube is the GUS assaybuffer (B.) Activity of reporter genes in C. macrophylla (a.) Picture ofpeeled phloem bark pieces of C. macrophylla infected with constructCTV33-23-BY-GFP-HC-GUS-51 under a fluorescent stereoscope (b.) Peeledbark phloem pieces GUS activity in infected and healthy C. macrophyllaplants (tubes 1 &2 represent the solution and tissues in fixing solutionfrom healthy leaves whereas 3&4 represent the solution and tissues frominfected leaves, respectively.

FIG. 15 Bimolecular Flourescence complementation (BiFC) proof ofconcept. (A) Schematic representation of CTVΔCla 333R (Gowda et al.,2001, Satyanarayana et al., 2003) replicon and its modification tocreate expression replicons: (a.) Insertion of both BiFC genes betweenp23 and 3′NTR giving rise to CTVp333R-23-BYbJunN-GbFosC and the controlswith one gene behind p23, CTVp333R-23-BYbJunN (b.) or CTVp333R-23-GbFosC(c.). (B) Northern blot hybridization analysis of transfected protoplastwith CTVp333R-23-BYbJunN-GbFosC (Lane a.), CTVp333R-23-BYbJunN (Lane c.)and CTVp333R-23-GbFosC (Lane b.). (C) Flourescence of a transfectedprotoplast when pictured under a stereoscope (Upper) or a laser scanningconfocal microscope (lower) indicating the flourescence from thenucleus.

FIG. 16 BiFC gene replacement of p13 to produce CTV based expressionvectors. (A) Schematic representation of CTV9RΔp33 and modification toproduce vector CTV33-Δ13-BYbJunN-GbFosC-76 and the control vectorsCTV33-23-G-bFosC-98 and CTV33-23-BY-bJunN-97 (insertion behind p23 nts19020-19021). (B) Representative sample of N. benthamiana fluorescencein systemically infected plants.

FIG. 17 CTV based expression vector built to simultaneously express twogenes from two controller elements. (A) Schematic representation ofCTV9RΔp33 and its modification to produce expression vectorsCTV33-23-BYbJunN-GbFosC-59 and CTV33-Δ13-BYbJunN-23-GbFosC-67. (B)Northern blot hybridization analysis of the RNA transfected protoplastwith the wild type virus (WT,T), two clones ofCTV33-Δ13-BYbJunN-23-GbFosC-67 (C67, T1 and T2) and two clones ofCTV33-23-BY-bJunN-Gb-FosC-59 (C59, T3 and T4) probed with 3′NTR+p23(Satyanarayana et al., 1999). (C) Flourescence of N. benthamiana plantparts under a fluorescent stereo microscope(CTV33-23-BY-bJunN-Gb-FosC-59=a., b., c. and d;CTV33-Δ13-BYbJunN-23-GbFosC-67=e.) (a.) bud (b.) Corolla, (c.) systemicleaves, (d.) peeled bark phloem pieces and (e.) infiltrated leaf

FIG. 18 CTV based expression vector built to simultaneously express twogenes from two controller elements. (A) Schematic representation ofCTV9RΔp33 and its modification to produce expression vectorsCTV33-Δ13-BYGUS-23-GGFP-71. (B) Northern blot hybridization analysis ofthe RNA transfected protoplast with the wild type virus (WT) and theCTV33-Δ13-BYGUS-23-GGFP-71 (C71) expression vector probed with 3′NTR+p23(Satyanarayana et al., 1999). (C) Biological activity of reporter genesin N. benthamiana and Citrus. N. benthamiana plant under white light(a.) and hand held UV light (b.). (c.) GUS activity from healthy (tube 1(assay solution) &2 (tissue) and infected N. benthamiana (tube 3 (assaysolution) and tube 4 (tissue). (d.) Peeled bark phloem pieces underfluorescent microscope and (e.) GUS assay activity in citrus similar to(c.)

FIG. 19 Western blot analysis of the different constructs in citrus toevaluate the expression of GFP and GUS. (A) GFP and CP antibody used todetermine the level of expression of GFP relative to CP in citrus 708plant infected with Δp33CTV9R (Tatineni et al., 2008), 1808 plantinfected with BCN5 (Folimonov et al., 2007), 1916 plant infected withCTV33-23-G-GFP-40, 1874 plant infected with CTV33-23-BY-GFP-37, 1934,1935, 1937 infected with CTV33-13-BY-GFP-69, 1931 and 1939 infected withconstruct CTV33-Δ13-G-GFP-65 and CTV33-Δ13-B-GFP-66, respectively. (B)GUS and CP antibody used to determine the level of expression of GUSrelative to CP in citrus 2084, 2085, 2086, 2087 plants infected withconstruct CTV33-Δ13-BYGUS-61, 2132 plant infected with constructCTV33-23-BYGUS-60, 2096 plant infected with expression vectorCTV33-Δ13-BYGFP-NIa-GUS-78, E=empty well and buffer=−iveC.

FIG. 20 CTV based expression vector built to simultaneously express fourgenes from four controller elements. (A) A schematic representation ofCTV9R. (B) Modification of CTV9R to create expression vectorCTVΔ13-BRFP-GbFosC-BYbJunN-CTMVCP-118 which expresses 4 genes fromdifferent locations within the CTV genome. The first gene is the redfluorescent protein gene (tagRFP) expressed from between the minor andmajor coat proteins under the control of the Beet yellows virus (BYV)coat protein controller element (CP-CE), the second and third genes arethe truncated mammalian transcription factors bFos and bJun fused to theC and N terminus of EYFP (Hu et al., 2002) under the control of Grapevine leaf roll associated virus-2 (GLRaV-2) and Beet yellow stunt virus(BYSV) CP-CE respectively replacing the p13 gene and the fourth gene isthe CP of TMV expressed from behind p23 under the control of theduplicated major CP-CE of CTV.

FIG. 21 CTV based expression vector built to simultaneously expressthree genes from three controller elements. (A) A schematicrepresentation of CTV9R. (B) Modification of CTV9R to create expressionvector CTVΔ13-GbFosC-BYbJunN-CTMVCP-129 which expresses 3 genes fromdifferent locations within the CTV genome. The first and second genesare the truncated mammalian transcription factors bFos and bJun fused tothe C and N terminus of EYFP (Hu et al., 2002) under the control ofGrape vine leaf roll associated virus-2 (GLRaV-2) and Beet yellow stuntvirus (BYSV) CP-CE respectively replacing the p13 gene and the fourthgene is the CP of TMV expressed from behind p23 under the control of theduplicated major CP-CE of CTV.

FIG. 22 CTV based expression vector built to simultaneously expressthree genes from three controller elements. (A) A schematicrepresentation of CTV9R. (B) Modification of CTV9R to create expressionvector CTV-BRFP-BYGFP-CTMVCP-117 which expresses 3 genes from differentlocations within the CTV genome. The first gene is the red fluorescentprotein gene (tagRFP) expressed from between the minor and major coatproteins under the control of the Beet yellows virus (BYV) coat proteincontroller element (CP-CE), the second gene is the Green fluorescentprotein (GFPC3) under the control of Beet yellow stunt virus (BYSV)CP-CE inserted between p13-p20 gene and the third gene is the CP of TMVexpressed from behind p23 under the control of the duplicated majorCP-CE of CTV.

FIG. 23 CTV based expression vector built to simultaneously expressthree genes from three controller elements. (A) A schematicrepresentation of CTV9R. (B) Modification of CTV9R to create expressionvector CTV-BASL-BYPTA-CP7-119 which expresses 3 genes from differentlocations within the CTV genome. The first gene is a lectin from Alliumsativum (ASL) expressed from between the minor and major coat proteinsunder the control of the Beet yellows virus (BYV) coat proteincontroller element (CP-CE), the second gene is an agglutinin fromPinellia ternata (PTA) under the control of Beet yellow stunt virus(BYSV) CP-CE inserted between p13-p20 gene and the third gene is anantimicrobial peptide from Tachypleus tridentatus (P7) expressed frombehind p23 under the control of the duplicated major CP-CE of CTV.

FIG. 24 CTV based expression vector built to simultaneously expressthree genes from three controller elements. (A) A schematicrepresentation of CTV9R. (B) Modification of CTV9R to create expressionvector CTV-BASL-BYPTA-CP10-120 which expresses 3 genes from differentlocations within the CTV genome. The first gene is a lectin from Alliumsativum (ASL) expressed from between the minor and major coat proteinsunder the control of the Beet yellows virus (BYV) coat proteincontroller element (CP-CE), the second gene is an agglutinin fromPinellia ternata (PTA) under the control of Beet yellow stunt virus(BYSV) CP-CE inserted between p13-p20 gene and the third gene is anantimicrobial peptide from Sus scorfa (P10) expressed from behind p23under the control of the duplicated major CP-CE of CTV.

FIG. 25 CTV based expression vector built to simultaneously expressthree genes from three controller elements. (A) A schematicrepresentation of CTV9R. (B) Modification of CTV9R to create expressionvector CTV-BASL-BYP10-CP7-131 which expresses 3 genes from differentlocations within the CTV genome. The first gene is a lectin from Alliumsativum (ASL) expressed from between the minor and major coat proteinsunder the control of the Beet yellows virus (BYV) coat proteincontroller element (CP-CE), the second gene is an antimicrobial peptidefrom Sus scorfa (P10) under the control of Beet yellow stunt virus(BYSV) CP-CE inserted between p13-p20 gene and the third gene is asecond antimicrobial peptide from Tachypleus tridentatus (P7) expressedfrom behind p23 under the control of the duplicated major CP-CE of CTV.

FIG. 26 CTV based expression vector built to simultaneously expressthree genes from three controller elements. (A) A schematicrepresentation of CTV91RΔp33. (B) Modification of CTV9R 433 to createexpression vector CTV33-BGFP-BYGUS-GTMVCP-79 which expresses 3 genesfrom different locations within the CTV genome. The first gene is agreen fluorescent protein expressed from between the minor and majorcoat proteins under the control of the Beet yellows virus (BYV) coatprotein controller element (CP-CE), the second gene is a β-Glucuronidase(GUS) gene from Eisherchia coli under the control of Beet yellow stuntvirus (BYSV) CP-CE inserted between p13-p20 gene and the third gene isthe CP of TMV expressed from behind p23 under the control of Grape vineleaf roll associated virus-2 (GLRaV-2) CP-CE.

FIG. 27 CTV based expression vector built to simultaneously express fourgenes from four controller elements. (A) A schematic representation ofCTV9RΔp33. (B) Modification of CTV9RΔp33 to create expression vectorCTV33-BGFP-GbFosC-BYbJunN-81 which expresses 3 genes from differentlocations within the CTV genome. The first gene is the green fluorescentprotein gene (GFPC3) expressed from between the minor and major coatproteins under the control of the Beet yellows virus (BYV) coat proteincontroller element (CP-CE), the second and third genes are the truncatedmammalian transcription factors bFos and bJun fused to the C and Nterminus of EYFP (Hu et al., 2002) under the control of Grape vine leafroll associated virus-2 (GLRaV-2) and Beet yellow stunt virus (BYSV)CP-CE respectively. The bFosC gene is inserted behind p23 gene.

FIG. 28 CTV based expression vector built to simultaneously express fourgenes from four controller elements. (A) A schematic representation ofCTV9RΔp33. (B) Modification of CTV9RΔp33 to create expression vectorCTV33-Δ13-BGFP-BYbJunN-GbFosC-82 which expresses 3 genes from differentlocations within the CTV genome. The first gene is the green fluorescentprotein gene (GFPC3) expressed from between the minor and major coatproteins under the control of the Beet yellows virus (BYV) coat proteincontroller element (CP-CE), the second gene is the truncated mammaliantranscription factor bJun to the N terminus of EYFP (bJunN) (Hu et al.,2002) under the control of Beet yellow stunt virus (BYSV) CP-Cereplacing the p13 gene of CTV and the third gene is the truncatedmammalian transcription factor bFos fused to the C-terminus of EYFP(bFosC) under the control of Grape vine leaf roll associated virus-2(GLRaV-2) CP-CE inserted behind p23.

FIG. 29 Negative staining Electron microscopy pictures from leaf dips ofinfiltrated N. benthamiana Leaves. (A) Leaf dips from infiltrated N.benthamiana leaves with construct CTV33-BGFP-BYGUS-GTMVCP-79 reveals theformation of CTV vector virions and TMV pseudo virions indicating theexpression of the TMV coat protein gene. (B) Leaf dip from InfiltratedN. benthamiana leaves with construct CTV33-Δ13-BGFP-BYbJunN-GbFosC-82reveals the formation of virions.

FIG. 30 Schematic representation of Citrus tristeza virus (CTV) genomein a binary vector. Schematic representation of full-length infectiouscDNA clones of Citrus tristeza virus (CTV) with its open reading frames(ORF) placed between enhanced 35S promoter of Cauliflower mosaic virusat the 5′ end, ribozyme (RZ) of Subterranean clover mottle virussatellite RNA and nopaline synthase terminator (Nos ter) at the 3′ endin the binary vector pCAMBIA-1380. The vector plasmid referred to aswild type CTV (CTV-wt) is based on CTV isolate T36. Unique restrictionsites, PacI and StuI at 5′ and 3′ end, respectively, to ligate theinserts under coat protein (CP) sub-genomic RNA controller element (CE)between ORF-p23 and 3′-nontranslated region (NTR). Truncated greenfluorescent protein (tGFP) was cloned using unique restriction sitesPacI and StuI to generate CTV-tGFP, similarly, truncated phytoenedesaturase (tPDS) and truncated abnormal wing disc (tAwd) were cloned togenerate CTV-tPDS and CTV-tAwd respectively. ORF p22 silencingsuppressor from Tomato chlorosis Crinivirus (ToCV) driven by 35Spromoter & 35s terminator (35S ter). PRO, papain-like proteases; MT,methyltransferase-like domain; HEL, helicase-like domain; RdRp,RNA-dependent RNA polymerase domain; and the ten 3′-end ORFs p33, p6,HSP70h, p61, CPm, CP, p18, p13, p20, and p23.

FIG. 31. Citrus tristeza virus (CTV)-induced gene silencing in Nicotianabenthamiana transgenic line 16c. Transgene green fluorescent protein(GFP) of Nicotiana benthamiana line 16c was silenced by Citrus tristezavirus (CTV)-based virus-induced gene silencing vector carrying truncatedGFP (tGFP). (a) Progression of GFP silencing in the systemic leaves,stems and flowers at 2, 3, 4 and 6 weeks post infiltration (wpi) wasphotographed under handheld long wave fluorescent UV lamp. GFP Silencedareas appear as red, indicated by arrow mark, due to autofluorescence ofchlorophyll. (b) Schematic representation of the subgenomic RNA (sgRNA)profile of CTV from plants infected with wild type CTV (CTV-wt) control(left), and CTV-tGFP (right). Abundantly accumulating sgRNAs for p23,p20 and CP are shown in thick lines. Northern blot shows the 3′ sgRNAsand the extra sgRNA for tGFP, indicated by a diamond symbol, accumulatedin CTV-tGFP plants (ii; on right) compared to CTV-wt plants (i; onleft). The blot was hybridized with digoxigenin labeled minus-senseribo-probe specific to the 3′-nontranslated region of CTV. (c)Accumulation of GFP-specific small interfering RNAs (siRNAs) in CTV-tGFPplants (ii) compared to CTV-wt (i). Ethidium bromide stained rRNA inpolyacrylamide gel electrophoresis as a loading control is shown at thebottom. Synthetic 5′-DIG-labeled oligonucleotide of 18 and 21 mer, whichran as 20 and 22 nucleotides, respectively, were used as siRNA sizemarkers (M). The blot was hybridized with digoxigenin labeledminus-sense ribo-probe specific to full-length sequence of GFP gene.

FIG. 32 Citrus tristeza virus (CTV)-induced gene silencing in citrus.Citrus macrophylla endogenous gene, phytoene desaturase (PDS) wassilenced by CTV-based virus-induced gene silencing (VIGS) vectorcarrying truncated PDS (tPDS). (a) Photo-bleaching phenotype observed inthe newly emerging leaves, stem and thorns, indicated by arrow marks (iiand iii), of C. macrophylla infected with CTV-tPDS compared to controlwild type CTV (CTV-wt) (i). (b) Northern blot shows the 3′ subgenomicRNAs (sgRNAs) and the extra sgRNA for tPDS, indicated by a diamondsymbol, accumulated in CTV-tPDS plants (ii; on right) compared to CTV-wtplants (i; on left). The blot was hybridized with digoxigenin labeledminus-sense ribo-probe specific to the 3′ nontranslated region of CTV.(c) Accumulation of PDS-specific small interfering RNAs (siRNAs) inCTV-tPDS plants (ii) compared to CTV-wt (i). Ethidium bromide stainedrRNA in polyacrylamide gel electrophoresis as a loading control is shownat the bottom. Synthetic 5′-DIG-labeled oligonucleotide of 18 and 21mer, which ran as 20 and 22 nucleotides respectively, were used as siRNAsize markers (M). The blot was hybridized with digoxigenin labeledminus-sense ribo-probe specific to full-length sequence of PDS gene.

FIG. 33 Graft-transmissibility of Citrus tristeza virus (CTV)-basedvirus-induced gene silencing (VIGS) vector and photo-bleaching phenotypeto other citrus cultivars. Source plant, Citrus macrophylla, harboringCTV-VIGS vector expressing truncated phytoene desaturase gene of C.macrophylla and inducing photo-bleaching phenotype. C. macrophyllasource plant used for side and leaf graft inoculations to Duncangrapefruit (C. paradisi) and Sour orange (C. aurantium), which inducedtypical photo-bleaching phenotype in the newly emerged systemic leaves.

FIG. 34. Citrus tristeza virus (CTV)-based plant-mediated RNAi inphloem-sap sucking insect Diaphorina citri. (a) Northern blot analysisof total RNA from systemic leaves of Citrus macrophylla plants infectedwith wild type CTV (CTV-wt) control (i) and truncated abnormal wing discgene (tAwd) expressing CTV vector (CTV-tAwd) (ii). Accumulation of anadditional subgenomic RNA (sgRNA), tAwd, in plants infected withCTV-tAwd is indicated by a diamond symbol. The blot was hybridized withdigoxigenin labeled minus-sense ribo-probe specific to the 3′nontranslated region of CTV. (b) Accumulation of Awd-specific smallinterfering RNAs (siRNAs) in CTV-tAwd plants (ii) in comparison toCTV-wt (i). Ethidium bromide stained rRNA in polyacrylamide gelelectrophoresis as loading control is shown at the bottom. Synthetic5′-DIG-labeled oligonucleotide of 18 and 21 mer, which ran as 20 and 22nucleotides respectively, were used as siRNA size markers (M). The blotwas hybridized with digoxigenin labeled minus-sense ribo-probe specificto full-length sequence of abnormal wing disc (Awd) gene. (c) Box plotshows the number of Diaphorina citri adults developed from nymphs fed onCTV-wt and CTV-tAwd plants after one month exposure. (d) Percentage ofwing-malformed adults on CTV-wt and CTV-tAwd plants, (e) expression ofAwd in D. citri adults exposed to CTV-wt and CTV-tAwd plants.Alpha-tubulin (TubA) and actin (Act) were used as a non-target gene andan internal control gene, respectively. The level of Awd transcripts inD. citri adults exposed to CTV-wt plants was arbitrarily set to thevalue one and the level of Awd transcripts in CTV-tAwd were presented asrelative value to this reference value. Means and standard deviation (asbars) of experiments in triplicate are presented. Asterisks indicatestatistically significant difference (p<0.05) and ‘ns’ asnon-significant. (f) Images of D. citri adults developed from nymphsafter exposure to CTV-wt (i) CTV-tAwd (ii) plants.

DETAILED DESCRIPTION

The early development of viral vectors was aimed at the inexpensiveproduction of high levels of specialty proteins that could be scaled upin the field. The first attempt at a plant viral vector utilizedCauliflower mosaic virus, a dsDNA virus (Brisson et al., 1984;Gronenborn et al., 1981). However, this vector was too unstable to beuseful (Fütterer et al., 1990). The development of reverse geneticssystems amenable for manipulation of RNA viruses made many more virusescandidates for vector development (Ahlquist et al., 1984). There wasconsiderable controversy concerning the value of RNA viruses for vectors(Siegel, 1983, 1985; Van Vluten-Dotting, 1983 Van Vluten-Dotting et al.,1985). It was argued that the lack of proof-reading of the RNA virusreplicases would result in too rapid sequence drift to maintain foreignsequences during replication. However, subsequent development and use ofRNA virus-based vectors demonstrated that this concern was overstated.

Ongoing efforts have been underway to create virus-based vectors forcitrus trees based on Citrus tristeza virus (CTV). CTV has the largestreported RNA of a plant virus of approximately 20 kb (Karasev et al.,1995; Pappu et al., 1994). It has two conserved gene blocks associatedwith replication and virion formation (Karasev, 2000). The replicationgene block occupies the 5′ half of the genome. Its proteins areexpressed from the genomic RNA via a poly protein strategy with a +1ribosomal frame shift to occasionally express the RNA dependent RNApolymerase (Karasev et al., 1995). The filamentous virions of CTV areencapsidated by two coat proteins, with the major coat protein (CP)encapsidating about 97% of the virion and the 5′ ˜700 nts encapsidatedby the minor coat protein (CPm) (Satyanarayana et al., 2004). Virionformation is a complex process requiring two proteins (Hsp70h and p61)in addition to the coat proteins (Satyanarayana et al., 2000, 2004;Tatineni et al., 2010). These four genes as well as the 6 remaininggenes are differentially expressed via a nested set of 3′ co-terminalsub genomic (sg) RNAs (Hilf et al., 1995). Upstream of each ORF there isa controller element (CE) that determines the transcription level (Gowdaet al., 2001). Levels of transcription are also associated with the +1transcription start site (Ayllón et al., 2003), the presence of anon-translated region upstream of the ORF (Gowda et al., 2001), and thecloseness of the ORF to the 3′ terminus (Satyanarayana et al., 1999).

The first generations of CTV vector examined three different strategiesthat were fusion of the CP gene, insertion of an extra gene, andreplacement of the p13 ORF (Folimonov et al., 2007). Replacement of thep13 ORF and fusion to the coat protein ORF did not result in effectivevectors, but the addition of an extra gene resulted in viable vectorsthat produce relative large amounts of foreign gene and were stable incitrus trees for years. However, the first efforts in designing vectorsbased on CTV examined only a few of the many possibilities forexpressing foreign genes in this large virus. In this work, theinventors attempted to examine the limitations of CTV to be manipulatedinto a vector. The inventors examined whether the virus allowedinsertions in different positions within the genome and which resultedin maximal expression with different sizes of inserts. The inventorsalso examined whether different fusion strategies with different viralgenes are viable and whether multiple foreign genes can be expressed.The CTV constructs disclosed herein are amazingly tolerant tomanipulation at several positions within the genome giving a multitudeof different vector strategies that are viable.

Once citrus is infected with a CTV vector containing a foreign gene, itis easy to move the vector to other citrus trees by grafting. However, alimitation of the CTV vector system is the difficulty of initiallygetting citrus infected with new vector constructs. Directly inoculatingcitrus from the cDNA clones, either by agro-inoculation, particlebombardment, or mechanical inoculation with RNA transcripts is extremelydifficult and unpredictable (Gowda et al., 2005; Satyanarayana et al.,2001). An alternative has been to inoculate with virions purified fromNicotiana benthamiana protoplasts (Folimonov et al., 2007; Robertson etal., 2005; Satyanarayana et al., 2001; Tatineni et al., 2008). However,infection of only approximately 0.01-0.1% of protoplasts with in vitrotranscribed RNA has been achieved (Satyanarayana et al., 2001). Yet,since virions are much more infectious to the protoplasts than RNA(Navas-Castillo et al., 1997), the inventors were able to amplify theinfection by sequential passage in protoplasts (Folimonov et al., 2007;Robertson et al., 2005; Satyanarayana et al., 2001; Tatineni et al.,2008). Although workable, this is an extremely difficult system. Theinventors are now able to agro-inoculate N. benthaminana plants thatresult in systemic infection. This result allows analysis of the vectorconstructs more quickly in these plants and provides copious amounts ofrecombinant virus for inoculation of citrus. Thus, the inventors reportthe activity of the different vector constructs in N. benthamina andCitrus.

According to one embodiment, the invention pertains to a CTV viralvector engineered to comprise a gene cassette comprising a heterologousnucleic acid. The gene cassette is located at a targeted position on theCTV genome. In a more specific embodiment, the CTV viral vector isengineered such that the gene cassette is positioned at CTV genomeregions p13-p20, p20-p23 or p23-3′NTR. In other embodiments, the CTVviral vector is engineered to include multiple genes at one or multiplepositions. It is shown herein that CTV viral vectors can successfully beengineered to include up to 3 or at least 4 genes that are expressibleby the vector, while maintaining the proper function and infectivity ofthe vector.

In related embodiments, the invention pertains to a plant that includesat least one cell transfected with the CTV viral vector engineered tocomprise a gene cassette comprising a heterologous nucleic acid, the CTVviral vector engineered such that one or more gene cassettes arepositioned at CTV genome regions p13-p20, p20-p23 or p23-3′NTR. Otherrelated embodiments pertain to methods of expressing at least oneheterologous nucleic acid or polypeptide in a plant by infecting theplant with the specified vector.

In a further embodiment, the invention is directed to a CTV viral vectorengineered to comprise at least one gene cassette that includes aheterologous nucleic acid, wherein the CTV viral vector engineered suchthat the gene cassette is inserted in place of the CTV p13 gene. Inrelated embodiments, the invention pertains to a plant that includes atleast one cell transfected with the CTV viral vector or to methods ofexpressing the heterologous nucleic acid or polypeptide in a plant byinfecting the plant with the specified vector.

In another embodiment, the invention relates to a CTV viral vectorengineered to comprise at least one gene cassette comprising apolynucleotide encoding heterologous polypeptide and IRES sequenceconjugated thereto. In related embodiments, the invention pertains to aplant that includes at least one cell transfected with the CTV viralvector or to methods of expressing the heterologous polypeptide in aplant by infecting the plant with the specified vector.

In further embodiments, the invention relates to a CTV viral vectorengineered to comprise a gene cassette comprising a polynucleotidesequence with continuous amino acid codons extending from the p23 ORFencoding a first heterologous polypeptide (protease) with cleavage siteson each side plus a second heterologous polypeptide. In relatedembodiments, the invention pertains to a plant that includes at leastone cell transfected with the CTV viral vector or to methods ofexpressing the heterologous polypeptide in a plant by infecting theplant with the specified vector.

In further embodiments, the polynucleotide further comprises a sequenceencoding a first control element upstream of said first heterologouspolypeptide, a second sequence encoding a protease with cleavage sitesengineered on each side, and a sequence encoding a second heterologouspolypeptide.

According to another embodiment, the invention is directed to CTV viralvector engineered to comprise a first gene cassette comprising apolynucleotide sequence encoding a first heterologous nucleic acid and afirst controller element upstream of said first heterologous nucleicacid encoding sequence; and a second gene cassette comprising apolynucleotide sequence encoding a second heterologous nucleic acid anda second control element upstream of said second heterologous nucleicacid encoding sequence. Optionally, the CTV viral vector furthercomprises a third gene cassette comprising a polynucleotide sequenceencoding a third heterologous nucleic acid and a third controllerelement upstream of said third heterologous nucleic acid encodingsequence; and a fourth gene cassette comprising a polynucleotidesequence encoding a fourth heterologous nucleic acid and a fourthcontroller element upstream of said fourth heterologous nucleic acidencoding sequence. Those skilled in the art will appreciate thatadditional gene cassettes can be added to the vector so long as functionand infectivity of the vector is maintained. In related embodiments, theinvention pertains to a plant that includes at least one celltransfected with the CTV viral vector or to methods of expressing theheterologous nucleic acid in a plant by infecting the plant with thespecified vector.

Examples of controller elements (CE) useful in accordance with theteachings herein include but are not limited to controller elementshomologous to CTV or heterologous control elements. Heterologouscontroller elements include, but are not limited to, coat proteincontroller elements (CP-CEs) of three closteroviruses: Beet yellowsvirus (BYV) (94 nts from 13547-13640 Genbank accession # AF190581)(Peremyslov et al., 1999), Beet yellow stunt virus (BYSV) (101 nts from8516-8616 Genbank accession # U51931) (Karasev et al., 1996) and Grapevine leaf roll associated virus-2 (GLRaV-2) (198 nts from 9454-9651Genbank accession # DQ286725). It will be evident to those skilled inthe art, in view of the teachings herein, that other controller elementsmay be implemented, and in particular control elements having strongpromoter like activity.

Silencing of Target Genes

Heterologous nucleic acid used to transfect plants may include nucleicacids that interact with a target nucleic acid. Namely, the heterologouspolynucleotide encodes a molecule able to modulate expression, RNAprocessing, translation or activity of a target nucleic acid. Theencoded molecule may be a RNA interfering molecule, antibody, antisensemolecule, PMO, ribozyme or small molecule.

RNA interference (RNAi) is a process by which double-stranded RNA(dsRNA) is used to silence gene expression. While not wanting to bebound by theory, RNAi begins with the cleavage of longer dsRNAs intosmall interfering RNAs (siRNAs) by an RNaselll-like enzyme, dicer.SiRNAs are dsRNAs that are usually about 19 to 28 nucleotides, or 20 to25 nucleotides, or 21 to 22 nucleotides in length and often contain2-nucleotide 3′ overhangs, and 5′ phosphate and 3′ hydroxyl termini. Onestrand of the siRNA is incorporated into a ribonucleoprotein complexknown as the RNA-induced silencing complex (RISC). RISC uses this siRNAstrand to identify mRNA molecules that are at least partiallycomplementary to the incorporated siRNA strand, and then cleaves thesetarget mRNAs or inhibits their translation. Therefore, the siRNA strandthat is incorporated into RISC is known as the guide strand or theantisense strand. The other siRNA strand, known as the passenger strandor the sense strand, is eliminated from the siRNA and is at leastpartially homologous to the target mRNA. Those of skill in the art willrecognize that, in principle, either strand of an siRNA can beincorporated into RISC and function as a guide strand. However, siRNAdesign (e.g., decreased siRNA duplex stability at the 5′ end of thedesired guide strand) can favor incorporation of the desired guidestrand into RISC.

The antisense strand of an siRNA is the active guiding agent of thesiRNA in that the antisense strand is incorporated into RISC, thusallowing RISC to identify target mRNAs with at least partialcomplementarity to the antisense siRNA strand for cleavage ortranslational repression. RISC-related cleavage of mRNAs having asequence at least partially complementary to the guide strand leads to adecrease in the steady state level of that mRNA and of the correspondingprotein encoded by this mRNA. Alternatively, RISC can also decreaseexpression of the corresponding protein via translational repressionwithout cleavage of the target mRNA.

The term “siRNA” as used herein refers to a double-stranded interferingRNA unless otherwise noted. Typically, an siRNA of the invention is adouble-stranded nucleic acid molecule comprising two nucleotide strands,each strand having about 19 to about 28 nucleotides (i.e. about 19, 20,21, 22, 23, 24, 25, 26, 27, or 28 nucleotides). The phrase “interferingRNA having a length of 19 to 49 nucleotides” when referring to adouble-stranded interfering RNA means that the antisense and sensestrands independently have a length of about 19 to about 49 nucleotides,including interfering RNA molecules where the sense and antisensestrands are connected by a linker molecule.

In addition to siRNA molecules, other interfering RNA molecules andRNA-like molecules can interact with RISC and silence gene expression.Examples of other interfering RNA molecules that can interact with RISCinclude short hairpin RNAs (shRNAs), single-stranded siRNAs, microRNAs(miRNAs), and dicer-substrate 27-mer duplexes. Examples of RNA-likemolecules that can interact with RISC include siRNA, single-strandedsiRNA, microRNA, and shRNA molecules containing one or more chemicallymodified nucleotides, one or more non-nucleotides, one or moredeoxyribonucleotides, and/or one or more non-phosphodiester linkages.All RNA or RNA-like molecules that can interact with RISC andparticipate in RISC-related changes in gene expression are referred toherein as “interfering RNAs” or “interfering RNA molecules.” SiRNAs,single-stranded siRNAs, shRNAs, miRNAs, and dicer-substrate 27-merduplexes are, therefore, subsets of “interfering RNAs” or “interferingRNA molecules.”

During replication of CTV, large amounts of double stranded RNAintermediates are produced of the genomic and subgenomic RNAs that areprocessed into small interfering RNA molecules. The subgenomic RNAs are3′-coterminal, so the more 3′ sequences are produced multiple times inthe longer subgenomic RNAs. Sequences designed to target specificsequences in the plant, pathogen, or pest do not need an extrasubgenomic mRNA controller element. Multiple target sequences can befused together as one larger heterologous sequence.

Single-stranded interfering RNA has been found to effect mRNA silencing,albeit less efficiently than double-stranded RNA. Therefore, embodimentsof the present invention also provide for administration of asingle-stranded interfering RNA that has a region of at leastnear-perfect contiguous complementarity with a portion of the targetnucleic acid. The single-stranded interfering RNA has a length of about19 to about 49 nucleotides as for the double-stranded interfering RNAcited above. The single-stranded interfering RNA has a 5′ phosphate oris phosphorylated in situ or in vivo at the 5′ position. The term “5′phosphorylated” is used to describe, for example, polynucleotides oroligonucleotides having a phosphate group attached via ester linkage tothe C5 hydroxyl of the sugar (e.g., ribose, deoxyribose, or an analog ofsame) at the 5′ end of the polynucleotide or oligonucleotide.

Single-stranded interfering RNAs can be synthesized chemically or by invitro transcription or expressed endogenously from vectors or expressioncassettes as described herein in reference to double-strandedinterfering RNAs. 5′ Phosphate groups may be added via a kinase, or a 5′phosphate may be the result of nuclease cleavage of an RNA. A hairpininterfering RNA is a single molecule (e.g., a single oligonucleotidechain) that comprises both the sense and antisense strands of aninterfering RNA in a stem-loop or hairpin structure (e.g., a shRNA). Forexample, shRNAs can be expressed from DNA vectors in which the DNAoligonucleotides encoding a sense interfering RNA strand are linked tothe DNA oligonucleotides encoding the reverse complementary antisenseinterfering RNA strand by a short spacer. If needed for the chosenexpression vector, 3′ terminal T's and nucleotides forming restrictionsites may be added. The resulting RNA transcript folds back onto itselfto form a stem-loop structure.

Nucleic acid sequences cited herein are written in a 5′ to 3′ directionunless indicated otherwise. The term “nucleic acid,” as used herein,refers to either DNA or RNA or a modified form thereof comprising thepurine or pyrimidine bases present in DNA (adenine “A,” cytosine “C,”guanine “G,” thymine “T”) or in RNA (adenine “A,” cytosine “C,” guanine“G,” uracil “U”). Interfering RNAs provided herein may comprise “T”bases, particularly at 3′ ends, even though “T” bases do not naturallyoccur in RNA. “Nucleic acid” includes the terms “oligonucleotide” and“polynucleotide” and can refer to a single-stranded molecule or adouble-stranded molecule. A double-stranded molecule is formed byWatson-Crick base pairing between A and T bases, C and G bases, andbetween A and U bases. The strands of a double-stranded molecule mayhave partial, substantial or full complementarity to each other and willform a duplex hybrid, the strength of bonding of which is dependent uponthe nature and degree of complementarity of the sequence of bases.

In certain embodiments, interfering RNA target sequences (e.g., si RNAtarget sequences) within a target mRNA sequence are selected usingavailable design tools. Interfering RNAs corresponding to a targetsequence are then tested in vitro by transfection of cells expressingthe target mRNA followed by assessment of knockdown as described herein.The interfering RNAs can be further evaluated in vivo using animalmodels as described herein.

Techniques for selecting target sequences for si RNAs are provided, forexample, by Tuschl, T. et al., “The siRNA User Guide,” revised May 6,2004, available on the Rockefeller University web site; by TechnicalBulletin #506, “siRNA Design Guidelines,” Ambion Inc. at Ambion's website; and by other web-based design tools at, for example, theInvitrogen, Dharmacon, Integrated DNA Technologies, Genscript, orProligo web sites. Initial search parameters can include G/C contentsbetween 35% and 55% and siRNA lengths between 19 and 27 nucleotides. Thetarget sequence may be located in the coding region or in the 5′ or 3′untranslated regions of the mRNA. The target sequences can be used toderive interfering RNA molecules, such as those described herein.

Many of the embodiments of the subject invention make reference toparticular methods of inhibiting or disruption of genetic expression.Based on the teachings herein, methods of inhibiting expression includebut are not limited to siRNA; ribozyme(s); antibody(ies);antisense/oligonucleotide(s); morpholino oligomers; microRNA; or shRNAthat target expression of the target nucleic acid. The subject inventionis not to be limited to any of the particular related methods described.One such method includes siRNA (small interfering/shortinterfering/silencing RNA). SiRNA most often is involved in the RNAinterference pathway where it interferes with the expression of aspecific nucleic acid. In addition to its role in the RNA interferencepathway, siRNA also act in RNA interference-related pathways, e.g., asan antiviral mechanism or in shaping the chromatin structure of agenome.

Another method by which to inhibit expression and to inhibit theexpression of the target nucleic acid in particular is shRNA. ShRNA(short hairpin or small hairpin RNA) refers to a sequence of RNA thatmakes a tight hairpin turn and is used to silence gene expression viaRNA interference. It uses a vector introduced into cells and a U6 or H1promoter to ensure that the shRNA is always expressed. The shRNA hairpinstructure is cleaved by cellular machinery into siRNA which is thenbound to the RNA-induced silencing complex. This complex binds to andcleaves mRNAs which match the siRNA that is bound to it.

Target nucleic acid can also be blocked by subjecting procured cells toan antibody specific to target nucleic acid or expression productthereof. An antisense nucleotide may also be used to block or inhibitexpression, in particular, the expression of target nucleic acid.Expression may also be inhibited with the use of a morpholino oligomeror phosphorodiamidate morpholino oligomer (PMO). PMOs are an antisensetechnology used to block access of other molecules to specific sequenceswithin nucleic acid. PMOs are often used as a research tool for reversegenetics, and function by knocking down gene function. This is achievedby preventing cells from making a targeted protein or by modifyingsplicing of pre-mRNA. One embodiment of the subject disclosure pertainsto a method of treating neurons under oxidative stress by expressing anRNA interfering molecule, antisense molecule or PMO in a subject in needthereof.

In one embodiment, the target nucleic acid may be endogenous in theplant transfected with the heterologous nucleic acid. Alternatively, theheterologous nucleic acid targets a nucleic acid that relates to a plantpathogen, a biological vector (e.g. insect that spreads pathogen), or anarthropod or nematode pest. For example, the heterologous nucleic acidencodes an RNA interfering molecule specific to a target nucleic acidrelating to a protein or sequence vital to the plant pathogen orbiological vector. This in effect neutralizes the pathogen or biologicalvector. Proteins or peptides can be to add value to the plant or toprevent attack by pest and pathogens. Examples of plant value-addedproducts include addition of vitamins or increase of flavor or stabilityto fruit or juice. Proteins or peptides can be to attract microbes orremove necessary microbes or to interfere with processes in pathogens orpests. RNAi targets can be the removal of any gene product in plants orprevention of protein production in pathogens or pests.

In addition to D. citri, almost any other insect could be a target togene silencing. Other insect pests of citrus are aphids and whitefliesthat vector viruses, mites (not an insect) that are a problem on theirown, as well as vector viruses, leaf miners that damage leaves andincrease susceptibility to canker, diaprepie roots weevils. Also, RNAican be used to control nematodes.

As far as other pathogens, other viruses and fungi could be controlledby RNAi. Value added traits can be induced by RNAi that allow forsilencing of undesired gene expression and gene products. For example,genes whose expression modulates flavor, color, or pathogen resistancecould be targeted.

These and other embodiments are further described below and encompassedwithin the appended claims.

Materials and Methods for Examples 1-7 Below

Plasmids Construction

pCTV9RΔp33 and pCTVΔCla 333R (Gowda et al., 2001; Satyanarayana et al.,1999, 2000, 2003; Tatineni et al., 2008) were used as base plasmids fordeveloping all expression vectors that were used in the protoplastreverse genetics system. The numbering of the nucleotides (nts) is basedon the full length T36 clone (Genbank Accession # AY170468)(Satyanarayana et al., 1999, 2003). CTVp333R-23-ITEV-GFP andCTVp333R-23-I3XARC-GFP (FIG. 7A) were created by fusing 5′ nontranslated region (NTR) of Tobacco etch virus (TEV) (nucleotides (nts)2-144 Genbank accession # DQ986288) (Carrasco et al., 2007) and 3xARC-1(Active ribosome complementary sequence) (Akergenov et al., 2004) behindthe p23 stop codon (between nts19020-19021 in full length T36 clone)using overlap extension polymerase chain reaction (PCR) (Horton et al.,1989). For creating expression vectors by gene addition and/orsubstitution at different locations, heterologous controller elements(CE) were selected from coat protein controller elements (CP-CEs) ofthree closteroviruses: Beet yellows virus (BYV) (94 nts from 13547-13640Genbank accession # AF190581) (Peremyslov et al., 1999), Beet yellowstunt virus (BYSV) (101 nts from 8516-8616 Genbank accession # U51931)(Karasev et al., 1996) and Grape vine leaf roll associated virus-2(GLRaV-2) (198 nts from 9454-9651 Genbank accession # DQ286725) to drivethe ORFs for cycle 3 GFP (GFP) (Chalife et al., 1994; Crameri et al.,1996), β-Glucuronidase (GUS) ORF of Eisherchia coli, bFosYC155-238(bFosC), bJunYN1-154 (bJunN). CTVp333R-23-BYbJunN-GbFosC,CTVp333R-23-BYbJunN, CTVp333R-23-GbFosC (FIG. 15A) were created byoverlap extension PCR from plasmids pBiFC-bFosYC155 and pBiFC-bJunYN155(Hu et al., 2002) and CTV9R (Satyanarayana et al., 1999; 2003). Sincetwo NotI sites exist within the bimolecular fluorescence genes (BiFC),the overlap extension PCR products were digested partially by Nodrestriction endonuclease. The PCR products were introduced into a StuIand NotI digested pCTVΔCla 333R (FIGS. 7A & 3-15A).

The expression vectors created in pCTV9RΔp33 were introduced into theCTV genome by digesting the plasmid with PstI (nts 17208-17213) and NotIor StuI (introduced behind 19,293 the final CTV nucleotide). Overlapextension PCR (Horton et al., 1989) was used to introduce theappropriate genes at the different locations. Replacement of the p13gene was done by deletion of nts 17293-17581 in the p13 ORF and (CE) byoverlap extension PCR (FIGS. 3-1A, 3-2A, 3-11A, 3-16A, 3-17A & 3-18A).Similarly, insertion between p13 and p20 (nts #17685-17686) (FIG. 3A),p20-p23 (nts #18312-18313) (FIG. 4A) and p23-3′NTR (nts #19020-19021)(FIGS. 3-5A, 3-6A, 3-13A, 3-16A, 3-17A & 3-18A) were done by overlapextension PCR. A hybrid gene created by fusing the GFP ORF (Chalife etal., 1994; Crameri et al., 1996) and GUS ORF separated by the HC-Proprotease motif (nts 1966-2411 Genbank accession # M11458)(Allison etal., 1985; Carrington et al., 1989) and its recognition sequence fusedto the N terminus of GUS (ATGAAAACTTACAATGTTGGAGGGATG (SEQ ID NO: 1)(nts 2412-2438 Genbank accession # M11458) (Allison et al., 1985;Carrington et al., 1989) (Amino acid sequence (A.A.) MKTYNVG↓GM) (SEQ IDNO: 2) (arrow indicate processing site) and C terminus of GFP(ATGAAGACCTATAACGTAGGTGGCATG) (SEQ ID NO: 3) was created and insertedbehind p23 (FIG. 13A) or as replacement of p13 (FIG. 3-11A) underdifferent controller elements. A similar hybrid gene was created byusing the NIa protease motif of TEV (nts 6270-6980 Genbank accession #M11458) (Allison et al., 1985) and its recognition sequence(GAGAATCTTTATTTTCAGAGT (SEQ ID NO: 4) (nts 8499-8519 Genbank accession #M11458) (A.A. ENLYFQ↓S) (SEQ ID NO: 5) (arrow indicate processing site)(Carrington and Dougherty, 1988) at C terminus of GFP andGAAAACCTATACTTCCAATCG (SEQ ID NO: 6) at N terminus of GUS). Theredundancy of the amino acid genetic code was used to eliminate completeduplication of the nucleotide sequences of the recognition motifs. Asimilar strategy was used to create a hybrid gene between p23 ORF andGFP ORF in construct CTV33-23-HC-GFP-72 and CTV33-23-NIa-GFP-73 (FIG.8). Switching the recognition motif of the proteases generated controlvectors CTV33-23-HCØ-GFP-74 and CTV33-23-NIaØ-GFP-75 (FIG. 8).

The binary plasmid pCAMBIACTV9R (Gowda et al., 2005) was modified toeliminate the p33 gene by deleting nts 10858-11660 (Satyanarayana etal., 2000; Tatineni et al., 2008) and introducing a SwaI site behind theribozyme engineered based on subterranean clover mottle virusoid (Turpenet al., 1993). PCR products amplified from the expression vectors in thepCTV9RΔp33 back-bone were introduced into the modified binary plasmidpCAMBIACTV9RΔp33 digested with PstI (Forward primer C-749) and SwaI(Reverse primer C-1894). When introducing the bimolecular fluorescencecomplementation (BiFC) genes into constructs CTV33-23-BYbJunN-GbFosC-59(FIG. 17), CTV33-Δ13-BYbJunN-23-GbFosC-67 (FIG. 17),CTV33-Δ13-BYbJunN-GbFosC-76 (FIG. 16), CTV33-23-GbFosC-98 (FIG. 16) andCTV33-23-BYbJunN-97 (FIG. 16) a primer was used switching the PstI tothe compatible NsiI (primer C-2085) for ease of cloning (the bFosC genesequence contains one PstI site while the bJunN gene sequence containstwo PstI sites). Preliminary screening for the right inserts in thedifferent expression vectors was done by restriction digestion using theappropriate enzymes. The junctions where the foreign genes wereintroduced into the expression vectors were confirmed by sequencing atthe Interdisciplinary Center for Biotechnology Research (ICBR)(University of Florida, Gainesville, Fla.). All primers are listed inTable 1-1.

TABLE 1-1 List of primers used in building expression vector Primer nameSequence 5′-3′* Description* C-749 AGT CCT CGA GAA 3′end of p18 (CTV T36CCA CTT AGT TGT clones nts # 17121-17145) TTA GCT ATCwith an added XhoI site before nt #17121) (downstream of this primerther exist within CTV genome a PstI site (nts 17208-17213 of CTV T36)used for cloning) (F.P.) C-1358 TTA TGC GGC CGC 3′end of 3′NTR (ntsAGG CCT TGG ACC 19,270-19,293 of CTV T36 TAT GTT GGC CCCclone) contain (StuI and CCA TAG NotI sites) (R.P.) C-1568TAA TCG TAC TTG 5′end of GFP (nls 1-21) AGT TCT AAT ATGwith extension into 3′ end GCT AGC AAA GGA of BYV CP IR (nts # GAA GAA13620-13640 Genbank Accession # AF190581) (F.P.) C-1894 GCC GCA CTA GTA3′end of 3′NTR (nts TTT AAA TCC CGT 19,262-19,293 of CTV TTC GTC CTT TAGT36 clone) with extensions GGA CTC GTC AGT that include a ribozyme ofGTA CTG ATA TAA subterranean clover GTA CAG ACT GGAvirusoid (underlined) CCT ATG TTG GCC (Turpen et al., 1993) andCCC CAT AGG GAC SwaI and SpeI restriction AGT G sites (R.P.) C-1973ATG GAT GAG CTC 5′end of 3′NTR(nts  TAC AAA TGA TTG19021-19043 of CTV T36  AAG TGG ACG GAA clone) with extension TAA GTT CC into GFP 3′ end (nts  700-720) (F.P.) C-1974 GGA ACT TAT TCC3′end of GFP (nts 700- GTC CAC TTC AAT 720) with extension intoCAT TTG TAG AGC 5′ end of 3′ NTR (nts  TCA TCC AT19021-19043 of CTV T36  clone) (R.P.) C-1975 GCA CGT TGT GCTGLRaV-2 intergenic region ATA GTA CGT GCC of CP (nts 9568-9651ATA ATA GTG AGT Genbank Accession GCT AGC AAA GTAnumber DQ286725) (F.P.) TAA ACG CTG GTG TTT AGC GCA TAT TAA ATA CTA ACGC-1976 CAG CTT GCT TCT BYSV CP intergenic region ACC TGA CAC AGTof (nts 8516-8616 TAA GAA GCG GCA Genbank accession # TAA ATC GAA GCCU51931) (F.P). AAA CCC TAA ATT TTG CAA CTC GAT CAA TTG TAA CCTAGA GCG AAG TGC AAT CA C-1977 TTT AGC GCA TAT 5′ end of GFP (nts 1-21)TAA ATA CTA ACG with extension into the ATG GCT AGC AAA3′end of GLRaV-2 CP GGA GAA GAA intergenic region (nts 9628-9651 GenbankAccession number DQ286725) (F.P.) C-1979 ACT GTG TCA GGT3′end of p23 (nts 19,000- AGA AGC AAG CTG 19,020 of CTV T36 clone)TCA GAT GAA GTG with extension into 5′end GTG TTC ACGof BYSV CP IR (nts 8516- 8539 Genbank accession # U51931) (R.P.) C-1982TTG G AT TTA GGT Sp6 promoter (underlined GAC   ACT ATA G TGand italics) with 3′ end  GAC ATATGTTGG of 3′NTR (nts 19271-19293CCC CCC ATA of CTV T36 clone) used to develop dig labeled probe (R.P.)C-1983 GTA ACCTAG AGC 5′end of GFP (nts 1-23) GAA GTG CAA TCAwith extension into 3′end ATG GCT AGC AAA of BYSV IR of CP ( ntsGGA GAA GAA 8593-8616 Genbank Accession # U51931) (F.P.) C-1984GCC TAA GCT TAC 3X active ribosome AAA TAC TCC CCCcomplementary sequence ACA ACA GCT TAC (3XARC-1 nts 1-86 )AAT ACT CCC CCA (Akbergenov et al., 2004) CAC AGC TTA CAA (F.P.)ATA CTC CCC CAC AAC AGCTTG TCG AC C-1985 CTC CGT GAA CAC 5′end of TEV 5′NTR (nts CACTTC ATC TGA 1-21 Genbank Accession #AAA TAA CAA ATC M11458) with extension TCA ACA CAA into 3′end of p23 (nts 18997-19020 of CTV T36 clone) (F.P.) C-1986TTG TGT TGA GAT 3′end of p23 (nts 18997- TTG TTA TTT TCA19020 of CTV T36 clone) GAT GAA GTG GTG with extension into 5′ endTTC ACG GAG of TEV 5′ NTR (nts 1-21 Genbank Accession # M11458) (R.P.)C-1989 GGA GTATTT GTA 3′end of p23 (nts 18997- AGCTTA GGC TCA 19020 of CTV T36 clone) GAT GAA GTG  with extension into 5′endGTGTTC ACG GAG of 3XARC-1 (nts 1-21) (R.P.) C-1990 CCC CAC AAC5′end of GFP (nts 1-25) AGCTTG TCG ACA with extension into 3′endTGG CTA GCA AAG of 3XARC-1 (nts 66-86) GAG AAG AAC TTT (F.P.) C-2007CGT GAA CAC BYV 3′end of CPm and the CACTTC ATC TGAintergenic region of CP TTC GAC CTC GGT (nts 13547-13570 CGT CTT AGT TAAGenbank Accession # AF190581) with extension into p23 3′end (nts 19,000-19,020 of CTV  T36 clone) (F.P.) C-2008 TTA ACT AAG ACG3′end of p23 (nts 19,000- ACC GAG GTC GAA 19,020 of CTV T36 clone)TCA GAT GAA GTG with extension into the GTG TTC ACG 3′end of CPm and CPintergenic region of BYV (nts 13,547-13,570 Genbank Accession #AF190581) (R.P.) C-2009 GGC GAT CAC GAC GLRaV-2 3′end of CPmAGA GCC GTGTCA and 5′ end of CP ATT GTC GCG GCT intergenic region (ntsAAG AAT GCT GTG 9454-9590 Genbank GAT CGC AGC GCT Accession numberTTC ACT GGA GGG DQ286725) (F.P.) GAG AGA AAA ATA GTT AGT TTG TATGCCTTA GGA AGG AACTAA GCA CGT TGT GCT ATA GTA CGT GC C-2010TGA CAC GGC TCT  3′end of p23 (nts 19,000- GTC GTG ATC GCC 19,020 of CTV T36 clone) TCA GAT GAA GTG  with extension into theGTGTTC ACG 3′ end of GLRaV-2 CPm coding sequence (nts 9454-9477 GenbankAccession # DQ286725) (R.P.) C-2011 GCC ACC TAC GTT3′end of GFP (nts 697- ATA GGT CTT CAT 717) with extension intoTTT GTA GAG CTC the TEV HC-Pro protease ATC CAT GCCrecognition sequence (nts 2412-2435(genetic code redundancy used toeliminate dublication Genbank Accession # M11458) (R.P.) C-2012AAG ACC TAT AAC 5′ end of TEV HC-Pro GTA GGT GGC ATGprotease motif (nts 1959- AAG GCT CAATAT 1979 Genbank AccessionTCG GAT CTA # M11458) with extension into the HC-Prorecognition sequence (nts 2415-2438 genetic code redundancy used toeliminate duplication Genbank Accession # M11458) (F.P.) C-2013ATG AAA ACT TAC 5′end of GUS (nts 4-21) AAT GTT GGA GGGwith extension into the ATG TTA CGT CCT TEV HC-Pro recognitionGTA GAA ACC sequence and 3′ end of TEV HC-Pro proteasemotif (nts 2412-2438 Genbank Accession # M11458) (F.P.) C-2014GGT TTC TAC AGG TEV HC-Pro recognition ACG TAA CAT CCCsequence (nts 2412-2438 TCC AAC ATT GTA Genbank Accession # AGT TTT CATM11458) with extension into the 5′ end of GUS ORF sequence (nts 4-21)(R.P.) C-2015 CCG CAG CAG GGA 5′ end of 3′NTR (nts GGC AAA CAA TGA19021-19041 of CTV T36 TTG AAGTGG ACG clone) with extension intoGAA TAA GTT the 3′ end of GUS ORF (nts 1789-1812) (F.P.) C-2016AAC TTA TTC CGT 3′ end of GUS (nts 1789- CCA CTT CAA TCA1812) with extension into TTG TTT GCCTCC the 5′end of 3′NTR (ntsCTG CTG CGG 19021-19041 of CTV T36 clone) (R.P.) C-2017 CTT ACT CTG AAA3′end of GFP (nts 697- ATA AAG ATT CTC 717) with extension intoTTT GTA GAG CTC the 5′end of TEV-NIa ATC CAT GCC protease recognitionsequence (nts 8499-8519 Genbank Accession # M11458) and 5′ end ofTEV NIa protease motif (nts 6270-6272 Genbank Accession # M11458) (R.P.)C-2018 AAA GAG AAT CTT 5′ end of TEV NIa TAT TTT CAG AGTprotease motif (nts 6270- AAG GGA CCA CGT 6290 Genbank AccessionGAT TAC AAC # M11458) with extension into its recognitionsequence (nts 8499-8519 Genbank Accession # M11458) and 3′ end ofGFP (nts 715-717) (F.P.) C-2019 CGA TTG GAA GTA 3′end of TEV NIa motif TAG GTT TTC TTG (nts 6961-6980 Genbank CGA GTA CAC CAA Accession #M11458) with TTC ACT CAT extension into NIa recognition sequence (nts8499-8519 Genbank Accession # M11458 genetic code redundancyused to eliminate duplication) (R.P.) C-2020 CAA GAA AAC CTA5′end of GUS with TAC TTC CAA TCG extension into the TEV NIaATG TTA CGT CCT recognition sequence (nts GTA GAA ACC 8499-8519 GenbankAccession # M11458 genetic code redundancy used to eliminateduplication) and 3′ end of (nts 6978-6980 Genbank Accession # M11458)(F.P.) C-2021 GTC ACT TTG TTT 5′end of BYSV CP IR (nts AGC GTG ACT TAG8516-8536 Genbank CAG CTT GCT TCT Accession # U51931) with ACC TGA CACextension into 3′end of  p18 (nts 17269-17292 of  CTV T36 clone) (F.P.)C-2022 GTG TCA GGT AGA 3′ end of p18 (nts 17269- AGC AAG CTG CTA17292 of CTV T36 clone) AGT CAC GCT AAA with extension into 5′ endCAA AGT GAC BYSV CP IR (nts 8516- 8536 Genbank Accession #U51931) (R.P.) C-2023 TTA GTC TCT CCA 5′end of BYSV CP IR (ntsTCT TGC GTG TAG 8516-8536 Genbank CAG CTT GCT TCT Accession #U51931) with ACC TGA CAC extension into the 3′end of p20 (nts 18286-18309 of CTV T36 clone) (F.P.) C-2024 GTG TCA GGT AGA3′end of p20 (nts 18286- AGC AAG CTG CTA 18309 of CTV T36 clone)CAC GCA AGATGG with extension into the 5′ AGA GAC TAAend of BYSV CP IR (nts 8516-8536 Genbank Accession # U51931) (R.P.)C-2025 ATG GAT GAG CTC 3′end of p13 ORF (nts TAC AAA TGA--17581-17604 of CTV T36 GTT TCA GAA ATT clone) with extension intoGTC GAATCG CAT the 3′end of GFP ORF (nts 700-720) (F.P.) C-2026ATG CGA TTC GAC 3′end of the GFP ORF (nts AAT TTC TGA AAC700-720) with extension TCA TTT GTA GAG into the 3′end of p13 ORFCTC ATC CAT (nts 17581-17604 of CTV T36 clone) (R.P.) C-2027ATG GAT GAG CTC 5′end of p23 IR (nts TAC AAA TGA GTT18,310-18,330 of CTV T36 AAT ACG CTT CTC clone) with extension intoAGA ACG TGT 3′ end of GFP (nts 700- 720) (F.P.) C-2028 ACA CGT TCT GAG3′end of GFP (nts 700- AAG CGT ATT AAC 720) with extension intoTCA TTT GTA GAG p23 IR (nts 18310-18330 CTC ATC CATof CTV T36 clone) (R.P.) C-2029 TTT AGC GCATAT 5′ end of HA TAG (21nts)TAA ATA CTA ACG in pHA-CMV carrying bFos ATG TAC CCATAC(AA 118-210)-YC (AA GAT GTT CCA 155-238) (Hu et al., 2002)with extension into the GLRaV-2 CP IR 3′ end (nts 9628-9651 GenbankAccession number DQ286725) (F.P.) C-2030 TGG AAC ATC 3′end of CPm GLRaV-2 GTATGG GTA CAT (nts 9628-9651 Genbank CGT TAGTAT TTAAccession number ATATGC GCT AAA DQ286725) with extension into 5′end of HA tag (21nts) in pHA-CMV carrying bFos (AA 118-210)-YC (AA 155-238) (Hu et al., 2002) (R.P.) C-2031 ACT GTGTCA GGT3′end EYFP-YC (AA 232- AGA AGC AAG CTG 238) (Hu et al., 2002) withTTA CTT GTA CAG extension into the BYSV CTC GTC CATCP 5′IR (nts 8516-8539 Genbank Accession # U51931) (R.P.) C-2032GTA ACCTAG AGC 5′end of FLAG tag (21nts) GAA GTG CAATCA from pFLAG-CMV2ATG GACTAC AAA carrying bJunN (Hu et al., GAC GAT GAC2002) with extension into the 3′end of BYSV CP IR (nts 8593-8616 GenbankAccession # U51931) (F.P.) C-2051 GTC ACT TTG TTT 3′end of GLRaV-2 CPmAGC GTG ACT TAG (nts 9454-9474 Genbank GGC GAT CAC GAC Accession #DQ286725) AGA GCC GTG with extension into 3′endof p18 (nts 17269-17292 of CTV T36 clone) (F.P.) C-2052 CAC GGC TCT GTC3′end of p23 (nts 19,000- GTG ATC GCC CTA 19,020) with extensionAGT CAC GCT AAA into the 3′end of GLRaV-2 CAA AGT GACCPm coding sequence (nts 9454-9474 Genbank Accession # DQ286725) (R.P.)C-2053 GTC ACT TTG TTT BYV 3′end of CPm and the AGC GTG ACT TAGintergenic region of CP TTC GAC CTC GGT (nts 13547-13567 CGT CTT AGTGenbank Accession # AF190581) with extension into 3′end of p18 (nts17269-17292 of CTV T36 clone) (F.P.) C-2054 ACT AAG ACG ACC3′end of p18 (nts 17269- GAG GTC GAA CTA 17292 of T36 CTV clone)AGT CAC GCT AAA with extension into BYV CAA AGT GAC 3′end of CPm and theintergenic region of CP (nts 13547-13567 Genbank Accession #AF190581) (R.P.) C-2055 CAC AAC GTC TAT 3′end of p13 ORF (ntsATC ATG GCC TAG 17581-17601 of CTV T36 GTT TCA GAA ATTclone) with extension into GTC GAA TCG the 3′end of EYFP-YN (AA147-154) from pFlag- CMV2 carrying bJun-YN (Hu et al., 2002) C-2056CGA TTC GAC AAT 3′end of EYFP-YN (AA TTC TGA AAC CTA147-154) from pFlag- GGC CAT GAT ATA CMV2 carrying bJun-YN GAC GTT GTG(Hu et al., 2002) with extension into the 3′end of p13 (nts 17581-17601 of CTV T36 clone) C-2057 GGC ATG GAC GAG3′end EYFP-YC (AA 231- CTG TAC AAGTAA 238) (Hu et al., 2002) withTTG AAGTGG ACG extension into 5′end of GAATAA GTT 3′NTR (nts 19021-19041of CTV T36 clone) C-2058 AAC TTA TTC CGT 5′end of 3′NTR (nts CCA CTT CAA TTA 19021-19041 of CTV T36  CTT GTA CAG CTCclone) with extension  GTC CAT GCC into 3′end EYFP-YC (AA 231-238) (Hu et al., 2002) C-2059 TCG CTC TTA CCTBYSV CP 5′IR (nts 8516- TGC GAT AAC TAG 8536 Genbank AccessionCAG CTT GCT TCT # U51931) with extension ACCTGA CACinto the 3′end of p13 (nts 17,662-17,685 of CTV T36 clone) (F.P.) C-2063GTA ACCTAG AGC 5′end of GUS ORF (nts 1- GAA GTG CAA TCA21) with extension into the ATG TTA CGT CCT 3′ end of BYSV CP IRGTA GAA ACC (with extension into the 3′end of BYSV CP IR (nts8593-8616 Genbank Accession # U51931) (F.P.) C-2064 GGT TTC TAC AGG3′end of BYSV CP IR (nts ACG TAA CAT TGA 8591-8616 GenbankTTG CACTTC GCT Accession # U51931) with CTA GGTTAC AAextension into the 5′end  of GUS ORF (nts 1-21) (R.P) C-2067CCG CAG CAG GGA 3′end of p13 (nts 17581- GGC AAA CAA TGA17601 of CTV T36 clone) GTT TCA GAA ATT with extension into theGTC GAATCG 3′end of GUS (nts 1789- 1812) (F.P.) C-2068 CGA TTC GAC AAT3′end of GUS (nts 1789- TTC TGA AAC TCA 1812) with extension intoTTG TTT GCCTCC the 3′end of p13 (nts CTG CTG CGG 12581-17601 of CTV T36clone) C-2069 GTG TCA GGT AGA 3′end of p13 (nts 17662- AGC AAG CTG CTA17685 of CTV T36 clone) GTT ATC GCA AGG with extension into 5′endTAA GAG CGA of BYSV IR CP 5′IR (nts 8516-8536 Genbank Accession #U51931) (R.P.) C-2070 ATG GAT GAG CTC 5′IR of p20 (nts 17686-TAC AAATGA AGT 17709 of CTV T36 clone) CTA CTC AGT AGTwith extension into the ACG TCT ATT 3′end of GFP (nts 700- 720) (F.P.)C-2071 AAT AGA CGT ACT 3′end of GFP (nts 700- ACT GAGTAG ACT720) with extension into TCA TTT GTA GAG the 5′IR of p20 (nts CTC ATC CAT 17686-17709 of CTV T36  clone) (R.P.) C-2085 GCG G ATGCAT3′end of p18 (nts 17201- TATTT GGTTTT 17245 of CTV T36 clone)ACA ACA ACG GTA with two point mutations CGT TTC AAA ATG(C-A(17205) and G- T(17210)) creating NsiI site to replace the PstIsite (F.P.) C-2087 AAG ACC TAT AAC 5′end of TEV HC-Pro GTA GGT GGC ATGprotease motif (nts 1959- AAG GCT CAA TAT 1979 Genbank AccessionTCG GAT CTA # M11458) with extension into the HC-Prorecognition sequence (nts 2415-2438 genetic code sequence redundancy wasused to eliminate duplication Genbank Accession # M11458 (F.P.) C-2088ATG AAA ACT TAC 5′end of GFP ORF(nts 4- AAT GTT GGA GGG21) with extension into  ATG GCT AGC AAA the TEV HC-Pro recognitionGGA GAA GAA sequence (nts 2412-2438 Genbank Accession # M11458) (F.P.)C-2089 TTC TTC TCC TTT TEV HC-Pro recognition GCT AGC CAT CCCsequence (nts 2412-2438 TCC AAC ATT GTA Genbank Accession # AGT TTT CATM11458) with extension into the 5′ end of GFP ORF sequence (nts 4-21)(R.P.) C-2091 GAG AAT CTT TAT 5′ end of TEV NIa TTT CAG AGT AAGprotease motif (nts 6270- GGA CCA CGT GAT 6291 Genbank AccessionTAC AAC C # M11458) with extension into its recognitionsequence (nts 8499-8519 Genbank Accession # M11458) (F.P.) C-2092GAA AAC CTA 5′end of GFP ORF (nts 1- TACTTC CAATCG23) with extension into  ATG GCT AGC AAA the TEV-NIa proteaseGGA GAA GAA CT recognition sequence (nts 8499-8519 genetic codesequence redundancy used to eliminate duplication Genbank Accession #M11458) (F.P.) C-2093 AGT TCT TCT CCT TEV NIa protease TTG CTA GC CATrecognition sequence (nts CGA TTG GAA GTA 8499-8519 genetic codeTAG GTT TTC sequence redundancy used to eliminate duplication GenbankAccession # M11458) with extension into the GFP ORF sequence (nts 1-23)(R.P.) C-2094 AAG ACCTAT AAC 5′ end of TEV-NIa GTA GGT GGC ATGprotease motif sequence AAG GGA CCA CGT nts 6270-6291 GenbankGAT TAC AAC Accession # M11458) with extension into the HC-Prorecognition sequence (nts 2415-2438 genetic code sequence redundancy wasused to eliminate duplication Genbank Accession # M11458 (F.P.) C-2095CCC TCC AAC ATT 3′end of TEV NIa protease GTA AGT TTT CATmotif(nts 6959-6981 TTG CGA GTA CAC Genbank accession # CAATTC ACTDQ986288) with extension into the TEV HC-Pro protease motif (nts 2415-2438 Genbank accession # M11458) (R.P.) C-2096 GAG AAT CTT TAT 5′end of TEV HC-Pro TTT CAG AGT AAG  protease motif (nts 1959-GCT CAATAT TCG  1979 Genbank Accession GAT CTA AAG #M11458) with extension into the TEV NIa proteaserecognition sequence (nts 8499-8519 Genbank accession # M11458) (F.P.)C-2097 CGA TTG GAA 3′end of HC-Pro protease GTATAG GTT TTCmotif (nts 2388-2411 TTC GGATTC CAA Genbank accession # ACCTGA ATG AACM11458) with extension into the TEV NIa proteaserecognition sequence (nts 8499-8519 Genbank accession # M11458)(R.P.)C-2098 GCC ACCTAC GTT 3′end of p23(nts 18997- ATA GGT CTT CAT19017 of CTV T36 clone) GAT GAA GTG with extension into theGTGTTC ACG GAG 5′end of TEV HC-Pro protease recognitionsequence (nts 2412- 2435(genetic code sequence redundancy usedto eliminate duplication) Genbank Accession # M11458) (R.P.) C-2099ACT CTG AAA ATA 3′end of p23(nts 18994- AAG ATT CTC GAT19017 of CTV T36 clone) GAA GTG GTGTTC with extension into theACG GAG AAC 5′end of TEV NIa protease recognition sequence (nts8499-8519 Genbank Accession # M11458 (R.P.) M-804 CAT TTA CGA ACG5′end of GFP (nts 1-20) ATA GCC ATG GCT with 3′end of TEV 5′NTRAGC AAA GGA GAA (nts 126-143 Genbank GAA Accession # M11458) (F.P.)

Polymerase Chain Reaction (PCR)

PCR was performed using diluted plasmids (1:50) as templates using VentDNA polymerase (New England Biolabs, Ipswich, Ma.) according to themanufacturer recommendations.

Agro-Injection/Infiltration

Agro-inoculation of Nicotiana benthamiana was performed according to theprocedure developed by Gowda et al., (2005) with minor modifications.Agrobacterium tumefaciens EHA 105 was transformed with the binaryplasmid containing CTV, variants (expression vectors) and silencingsuppressors (p19 of Tomato bushy stunt virus (Gowda et al., 2005); p24of GLRaV-2 (Chiba et al., 2007), P1/HC-Pro of Turnip mosaic virus(Kasschau et al., 2003) and p22 of Tomato chlorosis virus (Cañizares etal., 2008) by heat shock method (37° C. for 5 minutes) and subsequentlywere grown at 28° C. for 48 hours (hrs) on luria burtani (LB)(Sigma-Aldrich, St Louis, Mo.) plates supplemented with antibiotics(kanamycin (50 microgram (μg)/milliliter (ml)) and Rifampicilin ((50μg/ml)). The colonies (two individual colonies per construct) were grownovernight as seed cultures in LB medium supplemented with antibiotics.On the next day 0.5 ml of the seed culture was used to inoculate 35 mlof LB medium supplemented with antibiotics for overnight growth. Thebacterial culture was centrifuged at 6,000 rotation per minute (rpm) andresuspended in 10 milli molar (mM) MgCL₂ and 10 mM MES. The pellet waswashed with 10 mM MgCL₂ and 10 mM MES and suspended in induction medium;10 mM MgCL₂ and 10 mM MES containing acetosyringone at a finalconcentration of 150 μM. The suspension was incubated in the inductionmedium for at least 5 hrs before injection into the stem or infiltrationinto the abaxial (lower) surface of N. benthamiana leaves.

Plant Growth Conditions

N. benthmaiana plants maintained in a growth-room (21° C. with 16 hrs oflight in a 24 hr period) were used for agro-injection/agro-infiltrationfour weeks after transplanting.

Infection of Citrus Plants

Recombinant virions of CTV for infection of citrus plants were obtainedfrom infiltrated and/or systemic leaves of N. benthamiana. The virionswere partially purified and enriched by concentration over a sucrosecushion in a TL 100 or SW41 rotor (Robertson et al., 2005). Virions ofconstructs expressing two foreign proteins were concentrated two timesover a step gradient followed by a cushion gradient in SW28 and SW41rotors, respectively (Garnsey and Henderson, 1982). Inoculation ofcitrus plants was carried out by bark flap inoculation into 1-1.5 yearold Citrus macrophylla seedlings (Robertson et al., 2005) which weregrown in a greenhouse with temperatures ranging between approximately25-32° C.

Protoplast Preparation, Transfection, RNA Isolation and Northern BlotAnalysis

N. benthamiana leaf mesopyhll protoplasts were prepared according to theprocedure previously developed by Nava-Castillo et al., (1997). Surfacesterilized leaves from three week old N. benthamiana plants were gentlyslashed on the lower side with a sterile blade and incubated overnightin the dark (16-20 hrs) in 0.7M MMC (0.7M mannitol, 5 mM MES, 10 mMCaCl₂) supplemented with the 1% cellulose (Yakult Honsh, Tokyo, Japan)and 0.5% macerase pectinase enzymes (Calbiochem, La Jolla, Calif.).

Capped in vitro RNA transcripts from NotI or StuI linearized plasmid DNAwere generated (Satyanarayana et al., 1999) using Sp6 RNA polymerase(Epicentre Technologies, WI) and were transfected into the protoplastsusing PEG (poly ethylene glycol) as described by Satyanarayana et al.,(1999). Four days after transfection, protoplasts were used forpreparation of total RNA for northern blot hybridization analysis andisolation of virions. Protoplasts were pelleted in equal amounts in two1.5 ml eppendorf tubes. The first tube was flash frozen in liquidnitrogen and stored at −80° C. for isolation of virions to subsequentlyinoculate a new batch of protoplasts to amplify virions (Satyanarayanaet al., 2000). The second tube was used for RNA isolation by the buffardbuffer disruption of protoplasts followed by phenol: chloroform: isoamylalcohol (25:24:1) extraction and ethanol precipitation as previouslydescribed by Navas-Castillo et al., (1997) and Robertson et al., (2005).Total RNA was resuspended in 20 μl DNAse/RNAase free water and used inNorthern blot hybridization analysis as previously described byLewandowski and Dawson (1998). In brief, isolated RNA was heat denaturedin denaturing buffer (8.6% formaldehyde, 67% formamide in 1×MOPS (5 mMsodium acetate, 1 mM EDTA, 0.02M MOPS pH=7.0) separated in a 0.9%agarose gel in 1×MOPS containing 1.9% formaldehyde, and transferred ontoa nylon membrane (Boehringer Mannheim, Germany) by electroblotting.Pre-hybridization (at least 1 hr) and hybridization (overnight) werecarried out in a hybridization oven (Sigma-Aldrich, St. Louis, Mo.) at68° C. A 900 nts digoxigenin labeled RNA probe corresponding to the 3′end of the CTV genome (plus strand specific CTV RNA probe)(Satyanarayana et al., 1999) was used for hybridization except when theinsertion of the foreign genetic material was behind p23 in which case adigoxigenin labeled RNA probe was produced from PCR amplified DNA(reverse primer contain 3′NTR of CTV and SP6 phage promoter (C-1982)according to the manufacturer recommendation (Boehringer Mannheim,Germany) that is complimentary to the sequence inserted behind p23 inaddition to the 3′NTR sequence of CTV.

Western Blots

After powdering the plant tissue in liquid nitrogen via grinding in amortar and pestle, laemmli buffer (50 mM Tris-Cl, pH 6.8, 2.5%2-mercaptoethanol, 2% SDS, 0.1% bromophenol blue, 10% glycerol) wasadded (100 μl per 100 mg tissue). The sample was transferred to a 1.5 mlcentrifuge tube and boiled in a water bath for 3 minutes followed bycentrifugation at maximum speed for 2 minutes. The supernatant wastransferred to a new tube and stored at −20° C. until further use. Theelectrophoresis was carried out in a 12% SDS-Polyacrylamide gel(Bio-Rad, Hercules, Calif.) followed by two hours of semi-dry blottingto transfer the protein onto a nitrocellulose membrane (Bio-Rad,Hercules, Calif.). The membrane was blocked for 1 hr at room temperaturefollowed by incubation with the primary antibody of either CP (1:5000),GFP (1:100) (Clontech Laboratories, Palo Alto, Calif.) or GUS (1:1000)(Molecular probes, Eugene, Oreg.) for an hour followed incubation for 1hr in horseradish peroxidase conjugated donkey anti-rabbit secondaryantibody (1:10,000) (Amersham, Buckinghamshire, United Kingdom).Finally, the chemiluminescent system for western blot (Amersham,Buckinghamshire, United Kingdom) development on an X-ray film (Kodak,Rochester, N.Y.) was used according to the manufacturer recommendations.

Plant and Protoplast Photos

Plant pictures under UV or white light were taken with a Canon Camera(Canon EOS Digital Rebel XTi 400D, Lake Success, N.Y.). Close upfluorescent pictures of plant parts or protoplast were taken using afluorescent dissecting microscope (Zeiss Stemi SV 11 UV-fluorescencedissecting microscope, Carl Zeiss Jena, GmbH., Jena, Germany). Highresolution protoplast pictures were taken using a confocal scanningmicroscope (Leica TCS SL, Leica Microsystems, Inc., Exton, Pa.).

Enzyme Linked Immunosorbent Assay (ELISA)

Double antibody sandwiched ELISA was used according to the proceduredeveloped by Garnsey and Cambra (1991). A rabbit polyclonal antibody (1μg/ml) was used for coating the ELISA plate. The plant tissue sample wasdiluted at a 1:20 in PBS-T (phosphate buffer saline-1% Tween 20)extraction buffer. The detection antibody used was Mab ECTV 172 (1:100Kdilution).

GUS Assay

Citrus bark pieces or systemic leaves from Agro-inoculated N.benthamiana plants that were surface sterilized in alcohol (70% ethanol)followed by Sodium hypo chloride (10% solution) and washing three timesin sterile distilled water before staining for GUS. The samples wereincubated overnight in an EDTA-phosphate buffer (0.1M Na₂HPO₄, 1 mMNa₂EDTA) containing 1 mg/ml X-gluc (cyclohexylammounium salt: GoldBiotechnology, St Louis, Mo.). Fixing of the tissue was done in 95%ethanol: glacial acetic acid solution (3:1.

Example 1: Systems Used to Examine CTV-Based Expression Vectors

CTV-based expression vectors were examined in three systems, N.benthamiana mesophyll protoplasts as well as whole plants of N.benthaminia and Citrus macropylla. The full-length cDNA clone of CTV(pCTV9R) and a mutant with most of the p33 gene deleted (pCTV9RΔp33),which has a PstI restriction site removed making cloning easier andstill retaining the ability to infect most citrus varieties (Tatineni etal., 2008), was used for building constructs to infect whole plants.Relatively quick assays were done in N. benthamiana protoplasts, whichrequire constructs to be built in the SP6 transcription plasmid(Satyanarayana et al., 1999). A mini-replicon pCTVΔCla 333R (Gowda etal., 2001), with most of the 3′ genes removed, was convenient to use inprotoplasts. The ultimate goal to obtain citrus trees infected with thedifferent CTV expression vectors was much more difficult and timeconsuming. So far, agro-inoculate citrus trees has proven difficult.Thus, to avoid this difficulty virions are amplified and concentratedfor inoculation of citrus trees by stem-slashing or bark-flapinoculation (Robertson et al., 2005; Satyanarayana et al., 2001). N.benthamiana protoplasts can be inoculated with in vitro producedtranscripts of recombinant CTV constructs and the virus amplified bysuccessively passaging virions in crude sap through a series ofprotoplasts (Folimonov et al., 2007; Satyanarayana et al., 2001;Tatineni et al., 2008). Also, recombinant CTV can be amplified in N.benthamiana plants after agro-inoculation (Gowda et al., 2005). Thevirus can infect mesophyll cells of agro-inoculated areas of leaves, butas the virus moves systemically into upper non-inoculated leaves, it islimited to vascular tissues and usually induces vein clearing and latervein necrosis. All of the vector constructs were examined duringsystemic infection of N. benthamiana plants. Since CTV virions do notresuspend after centrifugation to a pellet, virions have to beconcentrated by centrifugation through a sucrose step gradient (Garnseyet al., 1977; Robertson et al., 2005). After inoculation, the tops ofcitrus plants were removed, and viral systemic infections were monitoredin new growth after 2-3 months. Once trees were infected, inoculum(buds, leaf pieces, or shoots) from the first infected plants was thenused to propagate new plants for experimentation. The whole processtakes approximately one year. For this reason, the inventors chose toexamine only the most promising vector constructs in citrus trees. Someof the later developed constructs are not yet in citrus.

Example 2: Addition of an Extra Gene at Different Locations within theCTV Genome

Insertions at the p13 Gene Site

The effective CTV vector developed previously (Folimonov et al., 2007)has the additional gene inserted between the two coat protein genes,positioning the foreign gene as the sixth gene from the 3′ terminus.Yet, the most highly expressed genes of CTV tend to be closer to the 3′terminus. Thus, it appeared that positioning an inserted gene closer tothe 3′ terminus could result in higher levels of expression. P13, thethird gene from the 3′ terminus, is a relatively highly expressed genethat is not necessary for the infection of most of the CTV host range(Tatineni et al., 2008; Tatineni et al., in preparation). Yet,replacement of the p13 ORF with the GFP ORF was not successful inprevious attempts (Folimonov et al., 2007). There were possible reasonsfor the failure. The previous construct was designed with the assumptionthat translation initiated at the first start codon, but the p13 ORF hasa second in-frame AUG. Translation might normally start at the secondAUG. However, fusion of the GFP ORF behind the second in frame AUG alsodid not express the reporter gene (Gowda et al., unpublished result). Asecond possibility is that the p13 controller element (CE) might extendinto the p13 ORF or that ribosome recruitment is directed from withinthe ORF. Here, the inventors deleted the p13 CE and ORF and inserted anew ORF behind a heterologous CE in the p13 position. The GFP ORFcontrolled by the CP-CE from BYSV (101 nts from 8516-8616 accession #U51931), GLRaV-2 (198 nts from 9454-9651 accession # DQ286725) or BYVwere engineered into pCTV9RΔp33 as a replacement for nts 17293-17581(CTV33-Δ13-BY-GFP-57, CTV33-Δ13-G-GFP-65, CTV33-Δ13-B-GFP-66respectively) (FIG. 1A). RNA transcripts were used to inoculate a seriesof protoplasts to determine whether the constructs could replicate andwhether virions formed sufficiently for passage in crude sap to a newbatch of protoplasts. The fluorescence of infected protoplasts (data notpresented) and northern blot hybridization analysis demonstrated thesuccessive passage of the expression vectors through the protoplasttransfers (FIG. 1B). Furthermore, the level of the GFP mRNA was similarto that of CP. Vectors sequences CTV33-Δ13-BY-GFP-57, CTV33-Δ13-G-GFP-65and CTV33-Δ13-B-GFP-66 then were transferred into the Agrobacteriumbinary plasmid for agro-inoculation of N. benthamiana plants. All threevectors infected and moved systemically in vascular tissue of the N.benthamiana plants as indicated by fluorescence in leaves, buds, flowersand corolla (FIG. 1C), vein clearing phenotype in early stages, as wellas confirmed by ELISA (Data not presented).

CTV33-Δ13-G-GFP-65 and CTV33-Δ13-B-GFP-66 were amplified and used toinoculate Citrus macrophylla plants. The initially infected plantsexhibited bright fluorescence in vascular tissue (FIG. 1D). Fluorescencecontinued in these plants 2 years after inoculation.

The GFP ORF (720 nts) was replaced with the GUS ORF (1812 nts) in thesame position to examine the expression of a larger foreign gene. TheBYSV CP-CE was selected to drive the GUS ORF in expression vectorCTV33-Δ13-BY-GUS-61 (FIG. 2A). RNA transcripts of this construct weretransfected into protoplast where the virus replicated and passagedefficiently from one protoplast batch to another as indicated bynorthern blot hybridization analysis (FIG. 2B). In addition, it revealedthat the level of accumulation of GUS mRNA was identical to the CP mRNA,and the CP and CPm mRNAs of vector were similar to that of the wild typevirus. Agro-inoculation of N. benthamiana plants revealed that theconstruct infected and spread throughout the vascular tissue of theplants based on GUS staining and confirmed by ELISA (Data not presented)and the vein clearing phenotype.

Virions isolated from infiltrated leaves of N. benthamiana plants ofCTV33-Δ13-BY-GUS-61 infected Citrus macrophylla plants as confirmed byELISA (Data not presented) and the bioactivity of the GUS protein (FIG.2C). The GUS gene was still biologically active in citrus 1.5 year afterinoculation.

Technically, the above constructs replaced a gene (p13) rather thanadded an extra gene. To examine a vector with an extra gene between p13and p20, the CP-CE of BYSV controlling the GFP ORF was inserted betweennts 17685-17686 to yield CTV33-13-BY-GFP-69 (FIG. 3A). This vectorshould produce an extra subgenomic RNA between the subgenomic RNAs ofp13 and p20. Vector CTV33-13-BY-GFP-69 was examined in N. benthamianaprotoplasts and plants. In the protoplast system, CTV33-13-BY-GFP-69replicated efficiently and was successfully passaged from one protoplastbatch to another demonstrating efficient replication and virionformation as indicated by fluorescence (Data not presented) and northernblot hybridization analysis (FIG. 3B). The foreign mRNA accumulated at arelatively high level but the CP mRNA was reduced. Similar to thereplacement of p13 constructs, agro-inoculation of the expression vectorCTV33-13-BY-GFP-69 into N. benthamiana plants enabled the new vector toinfect and spread throughout the vascular tissue (FIG. 3C).

Construct CTV33-13-BY-GFP-69 infected C. macrophylla plants as indicatedby strong fluorescence throughout the vascular tissue (FIG. 3C) andconfirmed by ELISA (Data not presented). The plants were stillfluorescencing 2 years after inoculation.

Insertion Between p20 and p23

To examine expression of a foreign gene closer to the 3′ NTR of CTV, anextra gene was inserted between the p20 and p23 genes (nts 18312-18313).The BYV or BYSV CP-CE was used to drive the GFP mRNA in two vectorsbased on T36 CTV9RΔp33 (CTV33-20-B-GFP-49 and CTV33-20-BY-GFP-58) (FIG.3-4A). The new vectors produced an extra sgRNA mRNA between the p20 andp23 sgRNAs (FIG. 4B). However, the accumulation of the p20 sg mRNA wassubstantially reduced. Both vectors replicated and were passaged inprotoplasts, but the protoplast passage was reduced as demonstrated byreduced numbers of cells with GFP fluorescence and northern blothybridization (FIGS. 4B &C). When both CTV33-20-B-GFP-49 orCTV33-20-BY-GFP-58 vectors were infiltrated into N. benthamiana leavesfor transient expression, the vectors replicated and produced abundantamounts of GFP as indicated by fluorescence (Data not presented) andwestern blot analysis (FIG. 4D). However, when agro-inoculated into N.benthamiana plants, the constructs replicated but movement into uppernon-inoculated leaves was random and often unsuccessful. Since systemicinfection of N. benthamiana plants was marginal, no attempt was made toinoculate citrus.

Insertion Between p23 and 3′NTR

The next position to be examined was to make the inserted gene the3′-most gene. Since CTV gene expression tends to be highest for genespositions nearer the 3′ terminus, this position could be expected toresult in the highest level of expression of a foreign gene(Navas-Castillo et al., 1997; Hilf et al., 1995). Although the 3′ NTRhas been analyzed (Satyanarayana et al., 2002a), it was not known whateffect an extra gene in this area would have on the efficiency ofreplication. The insertion of an extra gene between the CP gene and the3′NTR in Tobacco mosaic virus (TMV) and Alfalfa mosaic virus (AMV)failed to produce viable vectors (Dawson et al., 1989; Sánchez-Navarroet al., 2001). The CP-CE of BYSV, GLRaV-2 or BYV in front of the GFP ORFwas inserted between nucleotides 19020 and 19021 creating vectorsCTV33-23-BY-GFP-37, CTV33-23-G-GFP-40 and CTV33-23-B-GFP-42,respectively (FIG. 5A). All of the constructs when transfected into theprotoplast replicated and were passaged efficiently as indicated bynorthern blot hybridization analysis (FIG. 5B) and GFP fluorescence(Data not presented). The GFP mRNA was the highest accumulating mRNA,with only slight decreases to the other mRNAs compared to that of thewild type virus (FIG. 5B). Furthermore, the constructs with a GFPinsertion 3′ of the p23 ORF had the highest accumulation of the foreigngene mRNA among the constructs examined. CTV33-23-BY-GFP-37,CTV33-23-G-GFP-40 and CTV33-23-B-GFP-42 constructs were agro-inoculatedinto N. benthamiana plants. The infections spread systemicallythroughout the vascular tissue as demonstrated by the fluorescence (FIG.5C), phenotype (vein clearing followed by necrosis), and ELISA (Data notpresented). The fluorescence in the vascular tissue of N. benthamianaplants was extremely bright and continued for the life of the infectedplants (FIG. 5C)

Construct CTV33-23-BY-GFP-37 was amplified by passage through 12protoplast sets before citrus inoculation. C macrophylla plants thatwere bark-flap inoculated with the concentrated virions became infected.The infection of citrus was confirmed by fluorescence of GFP (FIG. 3-5D)and ELISA (Data not presented). Inoculation of citrus with constructsCTV33-23-G-GFP-40 was done via amplification in agro-inoculated N.benthamiana plants. The infection rate was in 1 of 4 C. macrophyllaplants as indicated by fluorescence (FIG. 5D) and confirmed by ELISA(Data not presented). Similar to N. benthamiana, citrus plants expressedbright fluorescence in the vascular tissue 12 weeks after inoculationand were still fluorescing 2.5 years later (FIG. 5D).

To examine the ability of the vector to express a larger gene at thisposition, the GUS ORF behind the BYSV CP-CE was inserted 3′ of the p23gene resulting in construct CTV33-23-BY-GUS-60 (FIG. 6A). The constructreplicated in successfully transfected protoplasts. However, theaccumulation levels of all the CTV subgenomic RNAs were decreasedprofoundly compared to the wild type virus as demonstrated by northernblot hybridization analysis (FIG. 6B). Also, the CTV33-23-BY-GUS-60construct passaged poorly in protoplasts (Data not presented). Yet,after agro-inoculation of N. benthamiana plants, the vector replicatedand moved systemically as demonstrated by the systemic symptoms (veinclearing followed by necrosis), ELISA (Data not presented) and GUSassays. The activity of GUS in the N. benthamiana plants wascontinuously produced in old and new leaves until the death of the plant(FIG. 7C). Similar to CTV33-Δ13-BY-GUS-61, the location between p23 and3′NTR was able to accommodate moderately to long genes albeit with adifferential effect on sg RNA levels of upstream genes (FIG. 5B & FIG.6B)

Concentrated virions from Construct CTV33-23-GUS-60 were used toinoculate C. macropyhlla plants, which became infected as confirmed byELISA (Data not presented) and activity of the GUS gene (FIG. 6C).Furthermore, GUS activity and western blot analysis revealed thepresence of the GUS gene in citrus 1.3 years after inoculation (FIG. 6C,FIG. 19).

Example 3: Production of an Extra Polypeptide without Producing an ExtraSubgenomic mRNA

Internal Ribosome Entry Site Strategy (IRES)

The Tobacco Etch Virus (TEV) IRES

The 5′NTR of TEV mediates cap independent translation of the viral mRNA.Studies on the 5′NTR of TEV demonstrate its ability to initiatetranslation at an internal ORF in a bi-cistronic mRNA (Gallie, 2001;Niepel and Gallie, 1999). The 5′NTR of TEV (nts 2-144 Genbank accession# DQ986288) was inserted into a CTV mini-replicon behind the p23 ORF(between nts 19020-19021) followed by the GFP ORF (CTVp333R-23-ITEV-GFP)(FIG. 7A) to examine whether a bicistronic subgenomic mRNA would workwith this virus. Although northern blot hybridization analysisdemonstrated that the mini-replicon replicated and produced abundantamounts of the bicistronic mRNA in transfected N. benthamianaprotoplasts (FIG. 7C), GFP fluorescence was not observed, suggesting alack of translation of the second ORF in the bicistronic mRNA. Theinventors also examined the 5′NTR TEV IRES construct in full length CTVin N. benthamiana protoplasts and plants. Construct CTV33-23-ITEV-GFP-41was passaged efficiently from protoplast to the next protoplast sets(FIG. 7B), indicating the good replication and formation of virions, butno fluorescing protoplasts were observed demonstrating that this IRESdid not work well in CTV (data not presented). This construct infectedand moved systemically in N. benthamiana plants based on the systemicsymptoms of vein clearing followed by necrosis and ELISA (Data notpresented), but no GFP fluorescence was observed under UV light (Datanot presented).

Active Ribosome Complementary Sequence (ARC) IRES

Insertion of an IRES consensus sequence obtained from analysis of hostand viral mRNAs (the engineered 3xARC-1 (86 nts) IRES (Akbergenov etal., 2004)) was next examined for activity in CTV. This IRES was fusedbehind the p23 ORF (nts 19020-19021) in both the CTV mini-replicon(CTVp333R-23-I3xARC-GFP) and Δp33CTV9R (CTV33-23-I3XARC-GFP-43) asdescribed above (FIG. 7 A). However, after infection of protoplasts andplants, no GFP fluorescence was observed even though the virusreplicated well in both (FIGS. 7B&C).

Poly-Peptide Fusion

P23, the highest expressed gene of CTV, is a multifunctional proteinthat is essential for citrus infection. P23 is a silencing suppressorand controls plus to minus RNA ratio in infected cells via an RNAbinding domain constituted of positive charged amino acid residues andZn finger domain present between amino acid 50-86 (Lopez et al., 2000;Satyanarayana et al., 2002b; Lu et al., 2004). In order to create a genefusion the HC-Pro or NIa protease motifs of TEV were selected to befused at the C-terminus of p23 (between nts 19017 and 19018) (FIG. 8).The protease recognition sequence of the HC-Pro and NIa was duplicatedbetween p23 and the protease and between the protease and GFP creatingvectors CTV33-23-HC-GFP-72 and CTV33-23-NIa-GFP-73, respectively (FIG.8). The processing of the protease motif from p23 should release the p23with 7 extra amino acids at its C-terminus in the case of HC-Pro and 6amino acids in the case of NIa. The GFP protein should have two extraand one extra amino acid after being cleaved from HC-Pro and NIa,respectively. The recognition sequences were switched between HC-Pro andNIa creating vectors CTV33-23-HCØ-GFP-74 and CTV33-23-NIaØ-GFP-75 ascontrols that are unable to be cleaved (FIG. 8). All the polypeptidefusion vectors were created in CTV binary vectors for infection ofplants because in protoplast it was shown that p23 fusion did not affectthe ability to replicate and pass between protoplast sets (Tatineni andDawson, unpublished result). In N. benthamiana infiltrated leaves, allconstructs fluoresced similarly to each other and to the free GFPconstructs behind p23 (FIG. 9A). Furthermore, western immune-blotanalysis from infiltrated leaves indicated a near-perfect processing ofthe reporter gene from the polypeptide fusion (FIG. 10). The GFP proteindid not localize to the nucleus unlike the fusion to p23 without aprotease processing releasing the reporter gene. Upon agro-inoculationof plants, only constructs with the protease and its homologousprocessing sites were able to move systemically into uppernon-inoculated leaves. The fluorescence in upper non-inoculated leaveswas weaker than those for the expression vectors CTV33-23-BY-GFP-37,CTV33-23-G-GFP-40 and CTV33-23-B-GFP-42 carrying GFP under its owncontroller element (FIG. 9B). Furthermore, it was easier to visualizefluorescence on the abaxial rather than the adaxial leaf surface (FIG.9C). Upon inoculation of citrus with construct CTV33-23-HC-GFP-72, oneplant became positive with relatively low ELISA value compared to others(Data not presented). The reporter gene activity was not detected.

Example 4: Production of More than One Extra Foreign Protein from CTVVectors

Use of Single Controller Elements to Express Multiple Proteins

In order to exploit the polypeptide strategy to express multiple genesdriven by the same controller element in a CTV based vector, a fusionpolypeptide was created consisting of GFP/Protease (Pro)/GUS. Twodifferent protease motifs were used in the different constructs, HC-Proand NIa, with their proteolytic motifs and recognition sequencesseparating GFP ORF from the GUS ORF (FIGS. 14A & 3-16) (Carrington andDougherty, 1988; Carrington et al., 1989). Theoretically, in case theNIa was the protease motif in the fusion, six extra amino acids arecoupled with the N-terminal protein (GFP) at its C-terminus whereas onlyone extra amino acid is added to the N-terminus of GUS. Similarly, whereHC-Pro was the protease within the fusion poly-peptide, 7 extra aminoacids are added to the C-terminus of GFP and two extra amino acids addedto the N-terminus of GUS. The fusion genes ranged in size between 3127and 3480 nts.

Replacement of p13 Gene

The two fusions of GFP/Pro/GUS described above were engineered into thep13 site of CTV in the agro-inoculation binary vector under the controlof the BYSV CP-CE (CTV33-Δ13-BYGFP-HC-GUS-77 with HC-Pro protease motifand CTV33-Δ13-BYGFP-NIa-GUS-78 with NIa protease motif) (FIG. 11A). Theconstructs were agro-inoculated to N. benthamiana for monitoring theability to systemically infect the plant and produce GUS and GFP. Bothgenes were produced based on their assays (FIG. 11 B). Westernimmune-blot analysis indicated the efficient processing of the GFPprotein from the polypeptide fusion (FIG. 10). The virus multiplied andspread to high titers in N. benthamiana plants as indicated by symptomdevelopment in the upper leaves (FIG. 11B) and ELISA. However, the levelof GFP fluorescence was less than that of vectors CTV33-Δ13-BY-GFP-57,CTV33-Δ13-G-GFP-65 and CTV33-Δ13-B-GFP-66 expressing the GFP alone andspread more slowly into the upper non-inoculated leaves than thosevectors (Data not presented). In N. benthamiana plants, overlappingfluorescence and enzymatic activity of GUS were demonstrated 7 monthsafter the injection of the construct revealing their stability (FIG.12).

Insertion Between p23 and 3′NTR

In an attempt to improve the expression level of GFP and GUS, the fusionpolypeptide was moved closer to the 3′NTR. The fusion gene with eitherBYSV, GLRaV-2 or BYV CP-CE with the protease of HC-Pro was insertedbetween p23 and 3′NTR referred to as CTV33-23-BY-GFP-HC-GUS-51,CTV33-23-G-GFP-HC-GUS-53 and CTV33-23-BY-GFP-HC-GUS-55 whereas with theNIa protease constructs were named, CTV33-23-BY-GFP-NIa-GUS-52,CTV33-23-G-GFP-NIa-GUS-54 and CTV33-23-BY-GFP-NIa-GUS-56, respectively(FIG. 13). After N. benthamiana plants were agro-inoculated, all theconstructs multiplied and spread into the upper non-inoculated leaves asindicated by GFP fluorescence (FIG. 14A) and GUS activity (FIG. 14A).Similar to constructs CTV33-Δ13-BYGFP-HC-GUS-77 andCTV33-Δ13-BYGFP-NIa-GUS-78, fluorescence overlapping with GUS enzymaticactivity was demonstrated 7 months after injection indicating thestability of the fusion. However, C. macrophylla plants infected withconstruct CTV33-23-BY-GFP-HC-GUS-51 revealed only faint fluorescence andalmost no GUS activity (FIG. 14B) and high ELISA values.

Example 5: Use of Multiple Promoters to Express Foreign GenesSimultaneously

Bimolecular Fluorescence Complementation (BiFC) in CTV.

For examination of the insertion of two CP-CE controlling differentORFs, the BiFC system, which produces visible fluorescence only when thetwo proteins accumulate in the same cell, was used. This system wasdeveloped using the bJun fused to N-terminus of EYFP (A.A. 1-154)(referred to as bJunN) and bFos ORF fused to C-terminus of EYFP (A.A.155-238) (referred to as bFosC) (Hu et al., 2002).

Both proteins are transported to the nucleus where they directlyinteract enabling the EYFP protein to regain its wild type foldingpattern and results in emission of fluorescence upon activation by ablue light source (Excitation wave length is 525 nm and emissionwavelength is 575 nm) (Hu et al., 2002). One or both components of BiFCwere introduced into the CTV mini-replicon 3′ of the p23 ORF (betweennts #19020 and 19021 Genbank Accession # AY170468) referred to asCTVp333R-23-BYbJunN, CTVp333R-23-GbFosC and CTVp333R-23-BYbJunN-GbFosC(FIG. 15 A). Northern blot hybridization analysis demonstrates thesuccessful transfection of all three constructs into N. benthamianaprotoplast (FIG. 15B). The two transcription factors interacted in theplant cell as demonstrated by nuclear fluorescence observed only inprotoplasts infected with CTVp333R-23-BYbJunN-GBFosC (FIG. 15C). It isworth noting that the size of the two inserted genes is approximatelyidentical to that of the GUS ORF.

As a control for the BiFC experiments, the inventors also introduced thegenes individually into Δp33CTV9R behind p23 creating vectorsCTV33-23-BYbJunN-97 and CTV33-23-GbFosC-98 so that only one componentwould be produced (FIG. 16B). Neither construct exhibited fluorescencein the nucleus.

Expression of Multiple Foreign Genes Simultaneously at the Same Location

P13 Replacement.

Both genes were introduced into a Δp33CTV9R (Satyanarayana et al., 1999,2000, 2003; Tatineni et al., 2008) as a replacement of the p13 gene(replacement of the nucleotides deleted between 17292 and 17581),resulting in CTV33-Δ13-BYbJunN-GbFosC-76 (FIG. 16A). Transfection ofprotoplasts with the RNA transcripts of CTV33-Δ13-BYbJunN-GbFosC-76resulted in the nuclear fluorescence of infected protoplasts (Data notpresented). Similarly, infiltrated leaves of N. benthamiana plants withfull length CTV33-Δ13-BYbJunN-GbFosC-76 emitted nuclear fluorescence(FIG. 16B). On the contrary, infiltrated leaves with constructsCTV33-23-BYbJunN-97 and CTV33-23-GbFosC-98 did not show any nuclearfluorescence (Data not presented). Monitoring stem phloem and leaf veinsof N. benthamiana plants infiltrated with CTV33-Δ13-BYbJunN-GbFosC-76seven weeks after infiltration revealed fluorescence of the vasculartissue indicating the ability of this construct to systemically infectupper leaves of N. benthamiana (FIG. 16B).

Insertion Between p23 and 3′NTR.

The next step was to examine expression of the two genes when positionedcloser to the 3′ terminus. The two gene components of the BiFC systemwere introduced into CTVΔp33 behind p23 (between nts #19020 and 19021),CTV33-23-BYbJunN-GbFosC-59 (FIG. 3-17A). Upon RNA transfection ofconstruct CTV33-23-BYbJunN-GbFosC-59, nuclear flourescence of infectedprotoplast was observed under the fluorescent microscope. However, itwas difficult to pass the new construct from one protoplast batch toanother, similar to GUS and the GFP/Pro/GUS fusion genes inserted at thesame location. Upon agro-infiltration of N. benthamiana plants withCTV33-23-BYbJun-GbFosC-59 in full length CTV, fluorescence was observedin infiltrated areas. Systemic symptoms similar to that expected forinfection of N. benthamiana by CTV was extremely delayed. However,monitoring upper non-inoculated leaves and phloem tissue of the stem atseven weeks after agro-infiltration of leaves revealed fluorescence ofnuclei of the vascular tissue, demonstrating systemic infection by thevector (FIG. 17C). These results confirmed by ELISA, indicate that theposition between p23 and 3′NTR can accommodate two extra genes withoutaffecting the ability of CTV to systemically invade the plants. Similarto both genes replacing p13 in construct CTV33-Δ13-BYbJunN-GbFosC-76there was a delay in the time frame of colonizing the upper vasculartissues by construct CTV33-23-BYbJunN-GbFosC-59. Nuclear fluorescence ofsystemic stem phloem tissue indicates that CTV33-Δ13-BYbJunN-GbFosC-76infected more cells than construct CTV33-23-BYbJunN-GbFosC-59 (FIG. 16B&FIG. 17C). This difference in the number of cells infected indicatesthe better ability of CTV33-Δ13-BYbJunN-GbFosC-76 to move in N.benthamiana as compared to CTV33-23-BYbJunN-GbFosC-59.

Example 6: Expression of Multiple Foreign Genes Simultaneously fromDifferent Locations

To express multiple foreign genes from two different positions, theinventors elected to replace the p13 gene and insert a second genebehind p23. CTV33-Δ13-BYbJunN-23-GbFosC-67 (FIG. 17A) was created viareplacement of the p13 gene with the BYSV CP-CE driving the bJunN ORFand the GLRaV-2 CP-CE controlling the bFosC ORF inserted between the p23ORF and the 3′NTR. CTV33-Δ13-BYbJunN-23-GbFosC-67 was transfected intoprotoplasts and Northern blot analysis revealed the replication of thevirus (FIG. 17B). However, accumulation of the p23 mRNA was greatlyreduced. CTV33-Δ13-BYbJunN-23-GbFosC-67 was agro-inoculated into N.benthamiana. The infiltration into the leaves indicated nuclearfluorescence of infected cells (FIG. 17C) which were much fewer innumber compared to constructs CTV33-Δ13-BYbJunN-GbFosC-76 andCTV33-23-BYbJunN-GbFosC-59. Isolation of virions from leaves andtransfection of protoplast was carried out resulting in nuclearfluorescence of infected protoplast indicating the successful formationof biologically active virions. However, systemic infection was notachieved in N. benthamiana as indicated by the lack of nuclearfluorescence in the stem and upper non-inoculated leaves of N.benthamiana and confirmed by ELISA.

In order to further study simultaneous multiple gene expression from thedifferent locations as above, CTV33-Δ13-BYGUS-23-GGFP-71 was engineeredsuch that the GUS ORF under the control of the BYSV CP-CE replaced thep13 gene (nts 17292-17582) and the GFP ORF under the control of theGLRaV-2 CP-CE was inserted between the p23 and 3′NTR (nts 19020 and19021) (FIG. 18A). RNA transcripts of CTV33-Δp13-BYGUS-23-GGFP-71 weretransfected into N. benthamiana protoplasts and northern blot analysisindicated efficient replication of the construct in protoplasts (FIG.18B). Leaf infiltration of N. benthamiana plants with constructCTV33-Δp13-BYGUS-23-GGFP-71 resulted in replication of the virus asindicated by visible fluorescence under a UV light and by GUS activity(Data not presented). The agro-inoculated plants began to exhibit GUSactivity and fluorescence in the upper non-inoculated leaves 6 weeksafter infiltration (FIG. 3-18C). The systemic infection of upper leaveswas slightly slower than constructs with only GFP alone. Also, thephenotype of vein clearing followed by necrosis associated with CTVinfection of N. benthamiana vascular tissue occurred later than that ofsingle gene vectors. The level of fluorescence when observed UV lightappeared to be slightly less than that of the single gene constructs.However, the GFP fluorescence was more in plants infected with constructCTV33-Δp13BYGUS-23GGFP-71, which was controlled by its own CE, comparedto that of the fusion in constructs (CTV33-23-BY-GFP-HC-GUS-51,CTV33-23-BY-GFP-NIa-GUS-52, CTV33-23-G-GFP-HC-GUS-53,CTV33-23-G-GFP-NIa-GUS-54, CTV33-Δ13-BYGFP-HC-GUS-77 andCTV33-Δ13-BYGFP-NIa-GUS-78). The activity of both genes continued untilthe death of the N. benthamiana plants. Similarly, in citrus theexpression of both genes were better than the same genes in constructsCTV33-Δ13-BYGFP-NIa-GUS-78 and CTV33-23-BY-GFP-HC-GUS-51.

Example 7: Level of Foreign Gene Expression of the Different Constructsin Citrus

It is difficult to directly compare foreign gene expression from thedifferent vectors in citrus due to the differences in the times ofinfection, the ages of the tissue and the effects of the insertedforeign gene cassette on the replication of the virus. Yet, proteinpresence in citrus is the best measure of expression level. Thus,western blot analysis was used to compare the relative level ofexpression of the different GFP and GUS constructs in citrus to that ofCP protein, a house keeping gene to determine the replication levels.Western blots using the GFP antibodies and the CP antibody revealed atrend which confirms the relative higher expression levels near the 3′end of the genome and a lower expression level when the inserted gene ismoved further away from the 3′ end with the exception for the insertionbetween p13 and p20 (FIG. 19A). In contrary, the GUS expression incitrus revealed a higher relative expression level as replacement of p13rather than insertion behind p23 (FIG. 19B).

Example 8: Multiple Gene Vectors

Plasmid Construction:

Three and four gene vectors were developed by introducing differentcombination of gene cassettes into the CTV genome at differentlocations. Three of the vectors were developed in CTV9RΔp33 in thepCAMBIA 1380 background (CTV33-BGFP-BYGUS-GTMVCP-79,CTV33-BGFP-GbFosC-BYbJunN-81 and CTV33-Δ13-BGFP-BYbJunN-GbFosC-82). Theother three three gene vectors (CTV-BASL-BYPTA-CP7-119,CTV-BASL-BYP10-CP7-131, CTV-BASL-BYPTA-CP10-120 andCTV-BRFP-BYGFP-CTMVCP-117) and one four gene vector(CTVΔ13-BRFP-GbFosC-BYbJunN-CTMVCP-118) were developed by modifyingCTV9R in the background of pCAMBIA1380 altered by replacing thehygromycin ORF with the p22 ORF of Tomato chlorosis virus. For the easeof cloning the PstI restriction site in p33 ORF in full length CTV9R waseliminated by introducing a silent mutation using overlap extension PCRusing primers 1749 and 1750 in combination with primer C-1436 and C-253followed by digestion of both the overlap PCR product and CTV9R withXmaI and PmeI. Most of the gene cassettes were introduced into theirlocations by overlap extension PCR using the primers listed in tablet.The only exception was the insertion of green fluorescent protein cycle3 in between the CPm and CP gene. Introducing the GFPC3 gene cassetteinto that location was done by restriction digestion of 9-47RGFP plasmidand point mutated CTV9R in pCAMBIA1380 with PmeI and PstI.

Expression of Three and Four Foreign Genes Simultaneously

After successfully expressing two genes in N. benthamiana and citruswith one and two different controller elements we are building vectorsto express three and four foreign genes from three and four differentcontroller elements, respectively. The reporter genes used in differentcombinations were the green fluorescent protein (cycle 3 GFP, GFPC3),red fluorescent protein (tag red fluorescent protein, RFP), Bimolecularfluorescence complementation using the bFos and bJun mammaliantranscription factors (Hu et al., 2002), β-glucuronidase (GUS) gene fromEscherichia coli and the Tobacco mosaic virus (TMV) coat protein gene(CP). Similarly, three gene vectors were built in different combinationsto express two antimicrobial peptides (AMPs) from Tachypleus tridentatusand Sus scorfa, Allium sativum lectin (ASL) and Pinellia ternataagglutinin (PTA). The three gene vectors were either expressed from twoor three locations within the CTV genome

Expression of Three Foreign Genes from Three Different LocationsSimultaneously:

Six vectors were built to express three foreign genes from threedifferent locations. The vectors were built to express the genes eitherfrom CTV9RΔp33 or full length CTV9R.

Vectors Built to Express Three Genes from Three Different Locations inCTV9RΔp33

Two vectors were built by inserting the three extra gene cassettes intoCTV9RΔp33 creating expression vectors CTV33-BGFP-BYGUS-GTMVCP-79 (FIG.26) and CTV33-Δ13-BGFP-BYbJunN-GbFosC-82 (FIG. 28).CTV33-BGFP-BYGUS-GTMVCP-79 expresses the three ORFs of GFP (insertionbetween CPm and CP), GUS (insertion between p13 and p20) and the coatprotein of TMV (insertion between p23 and 3′UTR) under the CP-CE of BYV,BYSV and GLRaV-2, respectively. CTV33-Δ13-BGFP-BYbJunN-GbFosC-82expresses the three ORFs of GFP (insertion between CPm and CP), bJunNORF (replacement of p13) and bFosC (insertion between p23 and 3′UTR)under the CP-CE of BYV, BYSV and GLRaV-2, respectively. The two vectorswere infiltrated into N. benthamiana leaves in combination withsilencing suppressors and inoculated into citrus using the procedure ofGowda et al., 2005. As leaves were cut and grinded to isolate virionsover 70% sucrose cushion gradient just 5 days after infiltration intothe N. benthamiana leaves it was not likely that these plants will getsystemically infected, thus they were discarded. The fluorescence ofinfiltrated leaves under hand held UV indicated the expression of theGFP protein in both CTV33-BGFP-BYGUS-GTMVCP-79 andCTV33-Δ13-BGFP-BYbJunN-GbFosC-82 indicating the ability of the createdvector to replicate in the N. benthamiana leaves. Electron microscopegrids prepared from leaf dips of infiltrated N. benthamiana leaves forconstruct CTV33-BGFP-BYGUS-GTMVCP-79 andCTV33-Δ13-BGFP-BYbJunN-GbFosC-82 indicated the formation of virions aprerequisite for the successful mechanical inoculation of citrusseedlings with CTV. Furthermore, in the case ofCTV33-BGFP-BYGUS-GTMVCP-79 and not CTV33-Δ13-BGFP-BYbJunN-GbFosC-82there was the formation of rod-shaped structures referred to as TMVpseudo-virions a characteristic of the expression of the TMV coatprotein.

Vectors Built to Express Three Genes from Three Different Locations inCTV9R

Four vectors were built to express three foreign genes from the samethree different locations within the CTV genome. The three locationsselected were insertion between CPm and CP, p13 and p20 and p23 and3′UTR. For the ease of cloning into the full length CTV infectious clonea the PstI site within the p33 ORF was eliminated by introducing asilent point mutation by overlap extension PCR. Three of the fourvectors were created by using different combinations of the two AMPs,ASL and PTA resulting in expression vectors CTV-BASL-BYPTA-CP7-119,CTV-BASL-BYP10-CP7-131 and CTV-BASL-BYPTA-CP10-120. The fourth vectornamed CTV-BRFP-BYGFP-CTMVCP-117 was created by inserting the ORFs ofGFP, RFP and TMV CP under the control of BYV, BYSV and duplicated CP-CEof CTV. All the vectors were infiltrated into N. benthamiana to monitorthe development of systemic infection. CTV-BASL-BYPTA-CP7-119 developedefficient systemic infection in 1 N. benthamiana plant. Plantsinfiltrated with vector CTV-BRFP-BYGFP-CTMVCP-117 revealed fluorescencein systemic leaves under hand held UV. Upon development of pronouncedsystemic infection, virions from CTV-BRFP-BYGFP-CTMVCP-117 will beconcentrated over a sucrose step gradient and a sucrose cushion in orderto inoculate citrus plants similar to the procedure recently followedfor vector CTV-BASL-BYPTA-CP7-119

Expression of Three Foreign Genes from Two Different LocationsSimultaneously:

Two vectors were created for the simultaneous expression of three genesfrom two different locations within the CTV genome. One vector was builtin CTV9RΔp33 creating expression vector CTV33-BGFP-GbFosC-BYbJunN-81whereas the other vector was built in full length CTV9R namedCTVΔ13-GbFosC-BYbJunN-CTMVCP-129.

Vector Built to Express Three Genes from Two Different Locations inCTV9RΔp33:

CTV33-BGFP-GbFosC-BYbJunN-81 (FIG. 27) was engineered through modifyingCTV9RΔp33 by inserting a single gene cassette between CPm and CP (GFPORF under the control of BYV CP-CE) and a double gene cassette (bFosCORF followed by bJunN ORF under the control of GLRaV-2 and BYSV CP-CE,respectively) as an insertion between p23 and 3′UTR. A 1:1 mixture of 4different silencing suppressors and CTV33-BGFP-GbFosC-BYbJunN-81 wereinfiltrated into N. benthamiana leaves. Electron microscopy from gridsof leaf dips revealed the formation of virions similar to constructsCTV33-BGFP-BYGUS-GTMVCP-79 and CTV33-Δ13-BGFP-BYbJunN-GbFosC-82. Inaddition, the infiltrated leaves revealed strong fluorescence under handheld UV light. Infiltrated leaves were used to concentrate virions on a70% sucrose cushion in an attempt to infect citrus seedlings.

Vector Built to Express Three Genes from Two Different Locations inCTV9R:

CTV9R was modified by inserting a double gene cassette (bFosC ORFfollowed by bJunN ORF under the control of GLRaV-2 and BYSV CP-CE,respectively) as replacement of p13 and a gene cassette (TMV CP ORFunder the control of the duplicated CP-CE) as an insertion between p23and 3′UTR creating expression vector CTVΔ13-GbFosC-BYbJunN-CTMVCP-129(FIG. 21). This vector is recently infiltrated into N. benthamianaleaves. After systemic infection of N. benthamiana the virions will beconcentrated to enable the inoculation of citrus plants.

Expression of Four Foreign Genes from Three Different LocationsSimultaneously:

In order to build the four gene vector we used four gene cassetteslocated at three different locations within the CTV genome. The RFP ORFwas introduced between CPm and CP under the control of the BYV CP-CE,the two BiFC components bFosC and bJunN under the control of GLRaV-2 andBYSV respectively were introduced as a replacement of the p13 gene andthe TMV ORF under the control of the duplicated CP-CE of CTV wasintroduced behind p23. The four gene vector namedCTVΔ13-BRFP-GbFosC-BYbJunN-CTMVCP-118 was infiltrated into the N.benthamiana leaves for the development of systemic infection. Uponsystemic infection virion concentration will be carried out over asucrose step gradient and cushion for the infection of the citrus trees.

Discussion Related to Examples 1-8

In this work, CTV constructs that are extraordinarily permissive inallowing insertion of foreign sequences at different places in the 3′portion of the genome are disclosed. Numerous different potential vectorconstructs to express foreign genes via additional subgenomic RNAs,di-cistronic mRNAs, or protease processing of fusion proteins werecreated and examined. Remarkably, most of these constructs functioned asvectors. Additionally, that the CTV constructs disclosed herein arecapable of simultaneously producing large amounts of multiple foreignproteins or peptides.

The ultimate goal was to develop high expressing and stable vectors forthe natural CTV host, citrus. Thus, virions were concentrated from N.benthamiana plants infected with 12 different constructs that spread andexpressed moderate to high levels of the foreign protein(s) and used toinoculate citrus. C macrophylla plants became positive for infectionbetween 6-60 weeks after inoculation depending on the insert length inthe virus and the amount of virions concentrated from the N. benthamianaleaves that were used for inoculation. Most of the constructs thatinfected citrus produced moderate levels of the reporter gene/s.

Several approaches were examined for expression of foreign genes fromCTV. The first approach was the “add-a-gene” strategy that involved theaddition or duplication of a controller element and an additional ORF,which resulted in an additional subgenomic RNA. The “add-a-gene”approach was developed initially in TMV via duplicating the CPsubgenomic promoter controlling a foreign gene (Dawson et al., 1989;Donson et al., 1991; Shivprasad et al., 1999). An advantage of thisstrategy is that it expresses the exact protein with no additional aminoacids added to the N or/and C terminus which could affect its biologicalactivity, at relatively high levels. However, there are limitations ofthis strategy that should be considered. Duplication of the controllerelement can lead to homologous recombination resulting in the loss ofthe gene of interest (Chapman et al., 1992; Dawson et al., 1989).Although this made the TMV insert unstable, it appeared to have littleeffect on the stability in CTV (Folimonov et al., 2007). The use of aheterologous controller element from related viruses stabilized the TMVinsertions. However, heterologous controller elements usually aredifferentially recognized by the replicase complex of the virus(Folimonov et al., 2007; Shivprasad et al., 1999). This observation canbe utilized to regulate the levels of desired gene expression(Shivprasad et al., 1999). An important consideration is that there canbe competition between the different subgenomic RNAs of a virus. WithTMV, the extra gene competed with the coat protein gene and the movementgene. There appeared to be a maximal capacity for production ofsubgenomic RNAs that was divided among the three RNAs. Manipulationsthat resulted in increases in one resulted in decreases in the others.One solution was to reduce coat protein production to allow optimalforeign gene and movement gene expression (Shivprasad et al., 1999;Girdishivelli et al., 2000). Yet, CTV subgenomic mRNAs appeared to bemuch less competitive (Folimonov et al., 2007; Ayllón et al., 2003).

In previous work, a CTV vector was created that expressed an extra genebetween the CP and CPm genes that was an effective and stable vector incitrus trees. The foreign gene was in position 6 from the 3′ terminus(Folimonov et al., 2007). The position of the extra gene was chosenarbitrarily. Here the inventors continued vector design in an attempt todefine the limits of manipulation of the CTV genome in producing extraproteins or peptides. The virus expresses its ten 3′ genes via sg mRNAs(Hilf et al., 1995). One rule of CTV gene expression is that genesnearer the 3′ terminus are transcribed higher than internal genes. Forexample, transcription of the p33 gene, which is at position 10 from the3′ terminus, is very low in its native position, but transcriptionbecame very high when the p33 gene was moved near the 3′ terminus(Satyanarayana et al., 1999). Thus, expression of foreign genes frompositions nearer the 3′ terminus might result in higher levels than fromthe position 6 arbitrarily chosen in the first vector (Folimonov et al.,2007). Yet, based on results from other viruses, only certain positionswithin the viral genome are likely to tolerate extra gene insertions.For example, with TMV or Alfalfa mosaic virus the location between CPand 3′NTR did not accommodate an insert (Dawson et al., 1989; Lehto andDawson, 1990; Sanchez-Navarro et al., 2001). Remarkably, almost all ofthe constructs with insertions in CTV within the p13 deletion, betweenp13 and p20, and between p23 and the 3′ NTR were viable. In contrast, itwas found that the only position the virus did not tolerate insertionswas between the p20 and p23 genes. It is possible that these insertionsinterfered with the transcription of either of the adjacent genes.

Another strategy to express foreign genes in a viral vector consists ofin-frame fusion of an ORF of interest to a viral ORF at either the N orC terminus. The two proteins can be released by engineering a proteaseand processing sites between the two proteins (Dolja et al., 1997;Gopinath et al., 2000). It was first adapted in the potyviridae, tobaccoetch virus (Dolja et al., 1992). The major advantage of polyproteinfusion strategy is that the foreign protein is expressed in 1:1 ratiowith the viral protein. A major limitation is that this process addsextra amino acids at the N and/or C termini of both proteins, which mayaffect their biological activities.

A series of constructs utilizing the HC-Pro or NIa proteases frompotyviruses to enable post translational processing of the engineeredpolyprotein to release free GFP, protease, and the p23 protein werecreated. These vectors were able to systemically infect N. benthamiana.The systemic movement of these constructs was slower than the expressionvector constructs containing only the GFP ORF as an extra gene. Theslower systemic movement and the lower levels of GFP expression in thesystemic leaves partially could be attributed to the extra C-terminalamino acids of p23 reduced its activity in RNA silencing suppression oramplification of viral RNAs or the protease processing delayed itsactivity. Although these constructs did not produce the maximal levelsof foreign protein, they were viable vectors expressing substantialamounts of GFP.

Upon identifying the locations within the CTV genome that couldaccommodate foreign gene inserts, strategies were designed to constructviral vectors that express multiple genes. The first strategy dependedon the use of a single controller element driving the transcription of apolypeptide gene. The fusion gene that consisted of GFP/Pro/GUS, rangedin size from 3127 nts to 3480 nts. Other strategies utilized two extraCEs to produce two extra sg RNAs simultaneously. This strategy gave theflexibility to insert the two genes in tandem in the same location or intwo different locations. Both strategies worked.

Heterologous protein expression in whole plant is usually accomplishedby development of transgenic plants by insertion of foreign DNA into theplastid or nuclear genome. Plastid transformation has been successfulfor only a few annual crops. Time and success of nuclear transformationvaries among the different crops. Certain plants are more recalcitrantto transformation and subsequent regeneration than others. There areother disadvantages, particularly in perennial crops. For example,citrus has a long juvenile stage after regeneration that prolongs thetime necessary to evaluate the horticultural characteristics and delaysthe time to commercial use. Another major disadvantage is thattransformation is limited to the next generation of plants.

The inventors have now developed a series of different CTV vectors, eachwith different characteristics that are more effective under specificconditions. For example, with the “add-a-gene” vectors, the inventorswould advocate the expression of a small gene in 3′ of the p23 gene inCTV for maximal expression. A medium gene could be more efficientlyexpressed from within the p13 area. A large gene probably would bebetter accommodated as an insertion between CP and CPm where it woulddisrupt the viral subgenomic RNAs less and result in better systemicinvasion of the plant. For expression of smaller proteins, peptides, orRNAs to target RNA silencing, it is possible that the virus couldaccommodate 3 or 4 different genes. Different combinations of extra sgRNAs and protease processing can be chosen. Although two foreignproteins have been produced from other viruses, CTV is unique inusefulness because of its stability. The original vector has beencontinuously producing GFP for 8 years.

The uses of the CTV based expression vector have evolved since itsinception. It was initially developed as a laboratory tool for citrusimprovement. The vector was designed to express potential genes fortransformation of citrus. Results of the effect of the heterologous genein citrus, particularly if the effect was expected in mature tissue orfruit, could be obtained by the virus years before results would comefrom direct transformation. However, conditions and needs of the citrusindustry have changed due to the invasion of a new bacterial diseasereferred to as Huanglongbing (HLB). This disease has spread so rapidlyand is so damaging that the survival of the citrus industry isthreatened. Initially, the CTV vector was used to identify antimicrobialpeptides with activity against the HLB bacterium for transformation intocitrus. However, the disease is spreading so rapidly that transgenicplants may not be available in time to save the industry. Due to theremarkable stability, the CTV vector now is being considered for use inthe field to protect citrus trees and to treat infected trees untilresistant transgenic plants become available. The CTV vector as a toolin the field to fight an invading disease of citrus is only one exampleof what viral vectors can do for agriculture. The possibilities are manyfor very stable vectors like those of CTV and perennial crops,particularly trees. Many trees are productive for 100 years or more.During the lifespan of the trees technologies changes and disease andpest pressures change. To improve trees by traditional transformationmethods requires removing all of the present trees from the field andreplanting. The use of a viral vector could add new genes to theexisting trees.

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Example 9

1. Introduction

Virus-based vectors for expressing foreign genes in plants are routinelaboratory tools (Porta and Lomonossoff, 2002 and Gleba et al., 2007),generally developed for short term laboratory experiments in herbaceousplants or for making specialty products in these plants. However, thedevelopment of vectors that stably express foreign genes for years hasopened up new opportunities in perennial plants (Folimonov et al., 2007,Kurth et al., 2012, Dawson and Folimanova, 2013 and Dolja and Koonin,2013). Virus-based vectors can be used to modify the existing generationof trees. One such opportunity is the use for field application toprotect against disease or to treat infected plants. For example, therapid spread of devastating disease of citrus, citrus greening alsoknown as huanglongbing (HLB), which is threatening the survival of thecitrus industry has changed the Citrus tristeza virus (CTV) vector froma laboratory tool to a potential management strategy for citrus groves(Hodges and Spreen, 2012 and National Research Council, 2010). At thistime, the one of the hopes for survival of the Florida citrus industryis the production of resistant or tolerant trees via transgene(http://www.nytimes.com/2013/07/28/science/a-race-to-save-the-orange-by-altering-its-dna.html?pagewanted=all&_r=0).But the time to make, evaluate, and amplify transgenic citrus trees istoo long to save the industry. The viral vector can be deployed morequickly and is being considered as an interim approach (NationalResearch Council, 2010).

The HLB disease manifestation requires both the phloem-limitedpathogenic bacterium, Candidatus Liberibacter asiaticus (CLas), andphloem feeding Asian citrus psyllid insect vector, Diaphorina citri(Halbert and Manjunath, 2004). The disease can be controlled bysuppressing either. Initial efforts have been to control the bacterium,but recent progresses in RNA interference (RNAi) in psyllids provideanother possible approach (El-Shesheny et al., 2013, Wuriyanghan andFalk, 2013 and Khan et al., 2013). It is now well-established thatdouble-stranded RNA (dsRNA)-mediated gene silencing mechanism isconserved in many eukaryotes (Geley and Müller, 2004, Gordon andWaterhouse, 2007, Fire, 2007 and Price and Gatehouse, 2008). Plant viralvectors have been utilized in virus-induced gene silencing (VIGS) byexploiting antiviral defense mechanism of the host plants (Ratcliff etal., 1997, Waterhouse et al., 2001 and Lu et al., 2003). The dsRNAsgenerated by viral RNA polymerases as intermediates during replicationspecifically are targeted by host defense machinery (Tenllado andDíaz-Ruíz, 2001 and Weber et al., 2006) thus, RNA viruses are inducersas-well-as targets of inherent RNA silencing machinery (Waterhouse etal., 2001). With VIGS vector carrying sequences of host gene, thedefense machinery is targeted against the corresponding host mRNAs.

CTV is a member of the genus Closterovirus of the familyClosteroviridae, the largest and the most complex plant viral family.Single-stranded RNA genome of ˜19.3 kb is encapsidated by two coatproteins (CP) making a long flexuous virions (2000 nm by 10-12 nm)(Bar-Joseph et al., 1979 and Karasev et al., 1995). CTV vector has beenshown to be an efficient expression vector capable of expressing morethan one foreign gene engineered at different positions in its genomeeither as extra gene or substitution of some non-essential genes usinghomologous and heterologous sub-genomic RNA (sgRNA) controller elements(Dawson and Folimanova, 2013 and El-Mohtar and Dawson, 2014). However,plant virus-based vectors are notoriously unstable and tend to revert towild type, with notable exception of CTV vector which has stablyretained a foreign gene for more than a decade in citrus plants (Dawsonand Folimanova, 2013). Many of the plant and animal viruses encode onesilencing suppressor whereas CTV has been shown to encode three distinctsuppressors of RNA silencing (Lu et al., 2004), which potentiallyprotect CTV with such a large RNA genome from antiviral silencingmachinery of the perennial woody citrus host. CTV open reading frames(ORFs) p23 and coat protein (CP) suppress the silencing pathway atintra- and inter-cellular level, respectively, while ORF p20, exhibitsboth at intra- and inter-cellular level silencing (Lu et al., 2004).There were serious concerns whether the CTV-based vector couldeffectively induce gene silencing. Yet, expression of sequencestargeting citrus endogenous phytoene desaturase (PDS) gene by CTV-basedvector resulted in photo-bleaching phenotype in citrus, thusdemonstrating CTV as a gene silencing vector.

CTV is limited to phloem and phloem-associated cells in citrus treeslike CLas bacterium. Since D. citri are phloem feeders, they probe andsuck phloem sap and existent alongside including CLas (when feeding on adiseased plant) and there by succor CLas transmission. This coincidentcohabitation in the phloem tissue could be exploited to develop a methodto combat HLB disease. In our previous study, in vitro topicalapplication of dsRNAs of truncated abnormal wing disc (tAwd) gene tonymphs of D. citri induced wing deformation and reduced survivability inadults, both positively correlated with Awd gene down regulation(El-Shesheny et al., 2013). We hypothesized that; if D. citri couldacquire the CLas bacteria from citrus phloem during feeding, it wouldacquire other components as well present in the phloem sap, such asvirions (like virions of phloem limited CTV), virion RNAs, dsRNAs, smallRNAs, etc. The objective of this study was to develop a novel method tomitigate HLB disease by controlling its insect vector, D. citri, throughCTV-based plant-mediated RNA interference (RNAi). In the present study,gene silencing capabilities of CTV was exploited to express silencingtriggers such as dsRNAs (replicative intermediates of both genomic andsubgenomic RNAs) and small-interfering RNAs (siRNAs) specific to D.citri endogenous Awd gene in citrus phloem and associated cells.Silencing the Awd gene increased adult mortality and induced malformedwing phenotype which potentially would affect ability of psyllids tovector CLas. CTV-RNAi vector would therefore be relevant for fast-trackscreening of candidate sequences for RNAi-mediated pest control. Byvirtue of time, labor and cost, CTV-RNAi could be answer to the slow anddifficult citrus transgenic approach in mitigating HLB. Besides it couldbe a valuable tool in functional genomics studies on citrus.

2. Materials and Methods

2.1. Plant Material

Nicotiana benthamiana plants were grown under controlled growth-roomwith temperature of 22-24° C., 16/8 h daylight cycle and 60% humidity.One year old seedlings (approximately two feet tall & stem of a pencilthickness) of Alemow (Citrus macrophylla), Duncan grapefruit (C.paradisi) and Sour orange (C. aurantium) were maintained under acontrolled greenhouse conditions at Citrus Research and EducationCentre, Lake Alfred, Fla.

2.2. Citrus Tristeza Virus (CTV)-Based Vectors

The infectious cDNA clone of Citrus tristeza virus (CTV isolate T36;GenBank accession no. AY170468) in the binary vector pCAMBIA-1380 wasused as base plasmid for engineering all the constructs used in thisstudy (Satyanarayana et al., 1999, Satyanayanana et al., 2001, Gowda etal., 2005 and El-Mohtar and Dawson, 2014). This plasmid referred to aswild type, CTV-wt, contained CTV genomic RNA between the duplicated 35Spromoter of Cauliflower mosaic virus in the 5′ end, a ribozyme sequenceof Subterranean clover mottle virus satellite RNA at the 3′ end. Uniquerestriction sites, PacI and StuI were engineered at 5′ and 3′ end,respectively, to ligate the inserts under coat protein (CP) sub-genomicRNA controller element (CE) between ORF-p23 and 3′-untranslated region.

To clone truncated fragment of green fluorescent protein (GFP) andgenerate CTV-tGFP, GFP gene coding fragment corresponding to the nts4-443 of the 30B-GFP-Cycle 3 (Shivprasad et al., 1999) was amplified bySpeedSTAR HS DNA polymerase (Takara Bio. Inc.) using primers GFP-PacI(5′-CGAGTTAATTAAGCTAGCAAAGGAGAAGAACTTTTCACTG-3′, SEQ ID NO. 86) andGFP-StuI (5′-GACAAGGCCTGAGTTATAGTTGTACTCGAGTTTGTGTC-3, SEQ ID NO. 87′) &CTV-GFP (Satyanayanana et al., 2001) as a template. The PCR product wasdigested with PacI and StuI restriction enzymes and cloned intosimilarly digested CTV-wt engineered with CTV CP CE and unique PacI andStuI sites to enable ligation of similarly digested tGFP product.

To clone truncated PDS gene (tPDS) and generate CTV-tPDS vector, primerswere designed based on C. sinensis PDS gene (Genbank accession no.DQ235261.1). The truncated fragment corresponding to the nucleotides4-395 of the PDS gene was amplified using total RNA from C. macrophyllaas a template by SuperScript® III One-Step RT-PCR System with Platinum®Taq DNA Polymerase (Life Technologies Corp.) and primers PDS-PacI(5′-CGAGTTAATTAAAGCCTTTGCTTCAGCGTTTCTGAAAGTGCTTTC-3′, SEQ ID No. 79) andPDS-StuI (5′-GACAAGGCCTGTCTCATACCAGTTCCCGTCCCCATCTTTCC-3′, SEQ ID NO.80). The PCR product was digested with PacI and StuI restriction enzymesand cloned into similarly digested CTV-tGFP by replacing tGFP with tPDSfragment.

The truncated fragment corresponding to the nucleotides 4-462 ofputative abnormal wing disc-like protein (Awd) gene (Genbank accessionno. DQ673407.1) of D. citri was amplified from the total RNA isolatedfrom the D. citri by SuperScript® III One-Step RT-PCR System withPlatinum® Taq DNA Polymerase (Life Technologies Corp.) using the primersAwd-PacI (5′-CGAGTTAATTAAGCCGAACCCAAGGAAAGAACTTTTCTCATG-3′, SEQ ID NO.81) and Awd-StuI (5′-GACAAGGCCTTTATTCATAGATCCAGGATTCACTGGCATTTG-3′, SEQID Na 82). The PCR product was digested with PacI and StuI restrictionenzymes and cloned into similarly digested CTV-tPDS vector plasmid byreplacing tPDS with tAwd fragment.

2.3. Agroinfiltration of CTV Constructs into N. benthamiana

Procedures for agroinfiltration of CTV constructs into N. benthamianawas followed as described previously (Gowda et al., 2005, Ambrós et al.,2011 and El-Mohtar and Dawson, 2014). ORF p22 silencing suppressor fromTomato chlorosis Crinivirus (ToCV) ligated in place of hygromycin genewas used in the binary vector pCAMBIA1380 to help establish the CTVinfection in the infiltrated leaves (El-Mohtar and Dawson, 2014).

2.4. CTV Virion Isolation and Inoculation to Citrus

Systemic leaves from N. benthamiana that tested positive for CTV byELISA, were harvested after 4-6 weeks post infiltration and used toisolate CTV virions for bark-flap inoculation of C. macrophylla asdescribed previously (Gowda et al., 2005 and Robertson et al., 2005). Anadditional ultracentrifugation step at 50,000 rpm for 60 min at 4° C.was carried out in Beckman Optima™ TL 100 to further concentrate thevirions.

2.5. Large RNA Northern Blot Hybridization

Total RNA was extracted from 100 mg of C. macrophylla tissues usingRNeasy Mini Kit (Qiagen) and used in large RNAs Northern hybridizationsas described previously (Satyanarayana et al., 1999). Thenegative-stranded riboprobe with digoxigenin-labeled UTP specific to3′-untranslated region of CTV genomic RNA (273 nucleotide long) was usedfor hybridization.

2.6. Small RNA Isolation

Total RNAs were extracted from 1 g of C. macrophylla tissue usingTRIzol® Reagent (Life Technologies Corp.) and was further purified byextracting 1-2 times with Phenol:Chloroform:IsoAmylAlcohol (25:24:1)(Chomczynski and Sacchi, 1987) and separated into large and small RNAfractions by following mirVana™ miRNA Isolation Kit (Life TechnologiesCorp.). To enrich small RNAs, the RNA sample was brought to 25% ethanolconcentration. The lysate/ethanol mixture was passed through aglass-fiber filter to immobilize large RNAs and the ethanolconcentration of the filtrate was increased to 55%, and passed through asecond glass-fiber filter to immobilize small RNAs. Both glass-fiberfilters were washed to elute small and large RNAs separately.

2.7. Small RNA Northern Blot Hybridization

Detection of small interfering RNAs (siRNAs) by Northern blot wasfollowed as described in the manual of mirVana™ miRNA Isolation Kit(Life Technologies Corp.) with few modifications. One μg small RNAenriched sample was run on a 15% denaturing polyacrylamide gel(urea/TBE) at 150 volts for 90-120 min or until the dye front reachesbottom of the gel. Semi-dry method was employed to transfer small RNAsto positively charged nylon membrane at 100 mA for 60 min and the RNAwas immobilized on membrane by UV crosslinking. Full-length cDNAsequence of GFP (720 bp), PDS (1662 bp) and Awd (462 bp) genes werecloned into pGEM®-T Easy Vector (Promega) and negative-strandedDIG-labeled riboprobes were generated using DIG RNA labeling mix (RocheApplied Science) and T7 RNA polymerase. These probes were furtherhydrolyzed into 50-100 nt long RNA pieces by treating with sodiumcarbonate buffer as described (Dalmay et al., 2000) and used forhybridization. Prehybridization and hybridization were done at 41° C.using ULTRAhyb™ solution (Life Technologies Corp.) of 10 mL per 100 cm²of membrane. The rest of the Northern protocol was followed as describedpreviously (Satyanarayana et al., 1999) except the high stringency washat 41° C. Synthetic 5′-DIG-labeled oligonucleotide of 18 and 21 mer,which ran as 20 and 22 nucleotides respectively, were used as siRNA sizemarkers in small RNA Northern blot hybridizations.

2.8. Reverse Transcription Quantitative PCR (RT-qPCR) for Plant Tissue

The large RNA isolated from mirVana™ miRNA Isolation Kit was used inSYBR Green-I based RT-qPCR to measure the level of down-regulation ofPDS mRNAs due to gene silencing by CTV-based silencing vector incomparison to CTV-wt control plants. Citrus actin (ACT) gene expressionwas used as an internal control to normalize gene expressions amongtreatments for RT-qPCR reactions. The level of PDS mRNA from controlplants infected with CTV-wt was arbitrarily set to a value of one (1)and the level of the PDS mRNA from plants infected with CTV-tPDS wasestimated as a relative number to this reference value (Hajeri et al.,2011). Similar procedures were followed to measure the level ofdown-regulation of GFP mRNAs from N. benthamiana line 16c due to genesilencing by CTV-tGFP vector.

2.9. Insect Bioassay

Asian citrus psyllid, D. citri used in this study were collected fromcitrus groves, Polk Co., Fla. and maintained on Valencia sweet orange,C. sinensis (L.) (Osbeck), at 28±1° C., 60±2% RH and 16/8 h photoperiod.One year old C. macrophylla seedlings (approximately two feet tall &stem of a pencil thickness) were used for insect bioassay. In feedingexperiments, each of the C. macrophylla seedling infected with eitherCTV-tAwd or CTV-wt control was exposed to 100 D. citri adults caged ininsect rearing cages (30 in.×15.5 in.×15 in.) and kept in growth roomsin conditions as described above. One-month post exposure, all adultsand nymphs were removed and egg masses were left. Two weeks later, newlyemerged adults were counted, collected and examined for wingmalformation and photographed using a Canon Power Shot S3IS digitalcamera, Leica M3Z stereomicroscope. Five replicative treatments for eachexperiment were used and compared statistically by the use of t test thenumber of adults with malformed wings to total adults.

2.10. Gene Expression Analysis in D. citri

Total RNA was isolated using TRIzol® Reagent (Life Technologies Corp.)from total of 10 D. citri for each treatment. Single-stranded RNA waspurified from the total RNA by ssDNA/RNA Clean & Concentrator™ (ZymoResearch) and expression levels of Awd was determined using SYBR Green-Ibased RT-qPCR in triplicate for each biological replicate. Alpha-tubulin(TubA) was used as a non-target gene control and we normalized geneexpression of actin (Act) to compare the relative gene expression levelsamong treatments. The level of Awd transcripts in D. citri adultsexposed to CTV-wt plants was arbitrarily set to the value one and thelevel of Awd transcripts in CTV-tAwd were presented as relative value tothis reference value (Hajeri et al., 2011). Means and standard deviationof experiments in triplicate are presented.

3. Results

3.1. CTV-Induced Gene Silencing in N. benthamiana Line 16c

N. benthamiana is a non-natural host of CTV. To demonstrate the genesilencing capabilities of CTV, transgene green fluorescent protein (GFP)of N. benthamiana line 16c was silenced by CTV-VIGS vector carryingtruncated GFP (tGFP; Supplementary data 1a). We engineered tGFP into CTVto express 400 nucleotides of GFP under CTV CP sgRNA controller element(CE) using unique PacI and StuI restriction sites (FIG. 30). N.benthamiana plants were inoculated with a binary plasmid vector carryingCTV-tGFP through agro-infiltration of fully expanded true leaves. Wildtype CTV (CTV-wt) was used as a control. Progression of GFP silencingwas monitored in the leaves, stems and flowers by fluorescenceobservation under long wave UV (FIG. 31a ). Northern blot analysis oftotal RNA from the systemic leaves showed accumulation of the extrasgRNA in CTV-tGFP plants compared to CTV-wt plants. The tGFP sgRNA wasthe most abundantly accumulated sgRNA and the tGFP sequence was presentas a component of all sub-genomic and genomic RNAs (FIG. 31b ). The GFPsilencing was further confirmed by reverse transcription quantitativePCR (RT-qPCR) showing 4-5-fold down-regulation of GFP mRNA (data notshown), the extent of GFP-mRNA down regulation does not represent a truevalue because the total RNA isolated for RT-qPCR represents a mixturefrom silenced and non-silenced regions. Further, Northern blotshybridization showed accumulation of GFP-specific ˜21 nucleotide smallinterfering RNAs (siRNAs) from plants infected with CTV-tGFP compared toCTV-wt control plants (FIG. 31c ).

3.2. CTV-Induced Gene Silencing in Citrus

To test the silencing induced by CTV in citrus, its natural host, citrusendogenous gene, phytoene desaturase (PDS) was targeted by CTV-VIGSvector carrying truncated PDS (tPDS; below). We engineered tPDS into CTVto express 392 nucleotides of PDS under CTV CP sgRNA CE using uniquePacI and StuI restriction sites (FIG. 30). N. benthamiana plants wereinoculated with a binary plasmid vector carrying CTV-tPDS throughagro-infiltration of fully expanded true leaves and wild type CTV(CTV-wt) was used as a control. CTV virions were isolated fromsymptomatic systemic leaves of N. benthamiana four weeks postinfiltration. C. macrophylla plants inoculated with CTV-tPDS virionsshowed a photo-bleaching phenotype in the newly emerging leaves, stemsand thorns (FIG. 32a ) compared to control CTV-wt plants. Northern blotanalysis of RNA showed accumulation of the extra sgRNA in CTV-tPDSplants compared to CTV-wt plants (FIG. 32b ). Further, RT-qPCR showed a2.5-3-fold down-regulation of PDS mRNA in infected leaves (data notshown). Additionally PDS-specific siRNAs were detected from plantsinfected with CTV-tPDS compared to CTV-wt (FIG. 32c ).

Graft-transmissibility of CTV-VIGS vector and photo-bleaching phenotypeto other citrus cultivars was tested. Source plant, C. macrophylla,harboring CTV-tPDS vector, used for side and leaf graft inoculations toDuncan grapefruit (C. paradisi) and Sour orange (C. aurantium), whichinduced photo-bleaching phenotype in the newly emerged systemic leaves(FIG. 33).

3.3. CTV-Based Citrus Plant-Mediated RNAi in Phloem-Sap Sucking InsectD. citri

The results presented above suggested that CTV vector could besuccessfully used as an efficient silencing vector. We designed CTV-RNAivector, CTV-tAwd, to express 459 nucleotides sequence of D. citri Awdgene (tAwd; below) in citrus similar to CTV-tPDS (FIG. 30). CTV-tAwdvirions were isolated from symptomatic systemic leaves of N. benthamianaand inoculated to C. macrophylla plants similar to CTV-tPDS. Northernanalysis of the total RNA isolated from newly emerged systemic leaves ofC. macrophylla plants, which were inoculated with CTV-tAwd, showed theaccumulation of an extra sgRNA for tAwd compared to CTV-wt (FIG. 34a ).Awd-specific siRNAs were detected in CTV-tAwd plants compared to CTV-wt(FIG. 34b ). One hundred adult D. citri (per plant) were allowed to feedon five individually caged C. macrophylla infected with CTV-tAwd.One-month post exposure, all D. citri adults and nymphs were removed andegg masses were left. Two weeks later, we calculated the total number ofresulting D. citri adults in the new generation. Statisticallysignificant differences (t test and evaluated at P<0.05) were observedin number of newly emerged adults between CTV-tAwd and CTV-wt plants(FIG. 34c ). Among the new generation of D. citri adults that emergedfrom nymphs, some displayed wing-malformed phenotype. Nearly 15% of thenymphs fed on CTV-tAwd plants developed into severe wing-malformedadults (FIGS. 34d and f -ii) and another 30% of nymphs developed varyingdegrees of wing-malformation.

Alpha-tubulin (TubA) and actin (Act) were used as a non-target controlgene and internal control gene, respectively to quantify Awd expressionlevel between the treatments by t-test analysis. TubA expression did notchange between treatments while Awd gene expression was down-regulatedapproximately 1.5-2-fold in wing-malformed adults of D. citri comparedto control D. citri (FIG. 34e ). Acquisition of CTV-specific dsRNAs byD. citri was confirmed by conventional two-step RT-PCR using sense orantisense primer generated cDNAs from RNAs isolated from D. citri fed onCTV-tPDS and CTV-tAwd plants (unpublished data).

4. Discussion

During replication, CTV accumulates abundant amounts of genomic andsub-genomic (sg) replicative intermediates as double-stranded RNAs(Dodds and Bar-Joseph, 1983 and Hilf et al., 1995) and copious amountsof siRNAs (Scott and Dawson, unpublished), the latter possibly theconsequence of antiviral silencing activity. The sgRNAs for ORFs closerto the 3′-ends accumulated in abundance compared to ORFs away from the3′-end (Navas-Castillo et al., 1997). Additionally, the sgRNAs for p23,p20 and CP with dedicated sgRNA controller elements are produced inhigher abundance compared to other sgRNAs (Hilf et al., 1995). It isthus possible to augment the abundance of silencing triggers, such asdsRNAs and siRNAs, by engineering sequence of interest at the 3′ end andfoster CTV as a gene silencing vector. We have demonstrated the genesilencing capabilities of CTV vectors by silencing transgene GFP in N.benthamiana line 16c and endogenous gene PDS in citrus. Thus, CTV-basedVIGS vector could be a useful tool for reverse genetics to study thefunctions of citrus genes involved in basic cellular functions,metabolic pathways, developmental biology, and plant-microbeinteractions.

The observations that the three RNA silencing suppressors do not preventCTV-induced gene silencing, that CTV accumulates to high levels inphloem and phloem-associated cells, that CTV produces large amounts ofdsRNAs, and that D. citri nymphs suck large amounts of fluid from thephloem of young shoots encouraged us to target psyllid genes usingCTV-based RNAi vector.

Bt (Bacillus thuringiensis) toxin expressing transgenic plants have beeneffectively controlling chewing insects such as lepidopteran andcoleopteran pests (Naranjo, 2011 and Shelton et al., 2002). However, forphloem sap-sucking insects, such as psyllids, aphids, whiteflies,planthoppers and plant bugs, pesticides are still the major method tocontrol (Walker and Allen, 2010 and Gatehouse and Price, 2011).Therefore, in order to control phloem sap-sucking insects, novelmethodologies such as RNAi-based technology must be considered in orderto rein in economic and environmental damage (Zhang et al., 2013).

The two major challenges in deploying RNAi-based technology for pestcontrol are effective target gene selection and reliable dsRNA delivery.We targeted D. citri endogenous Awd gene for silencing; because,inhibition of the Awd gene would induce altered wing development, avisible phenotype and down regulation of wing development of D. citriwould impair its ability to fly and potentially limit the successfulvectoring of the bacterial pathogen between citrus trees in the grove.Once the target gene is identified, the reliable and convenient dsRNAdelivery system is prerequisite for pest control at field level.Delivery of dsRNA could be achieved by micro-injection,micro-application (topical application), soaking or by feeding as adietary component (El-Shesheny et al., 2013 and Zhang et al., 2013).However, these methods can only be used in laboratory experiments.Spraying dsRNA targeting specific insect pest could be a viable approachat the field level (Gan et al., 2010), if dsRNA can be cheaply massproduced. Expression of dsRNAs in transgenic plants has been shown toinduce RNAi effects on target insects (Huang et al., 2006, Baum et al.,2007, Mao et al., 2007 and Gottula and Fuchs, 2009). However, transgenicapproach in citrus is slow and difficult. By virtue of its time, laborand cost efficiency, transient expression system of CTV-basedplant-mediated RNAi provides major advantage over stable transformationin citrus since the CTV vector has been shown to be stable for severalyears in trees. This remarkable stability of CTV vector could be used insilencing insect genes or other pest genes directly in the field as anintegrated pest management practice. Graft-transmissibility of CTV-tPDSvector and its silencing triggers to other citrus cultivars suggestedthat the silencing trait against insect pests induced by CTV-RNAi vectorcould also be transferable to other commercial cultivars of citrusthrough vegetative grafting which is not possible with transgenic lineswith such traits.

Even in case of preference of transgenic approach over CTV-based RNAi,the CTV vector would act as a tool in fast-track screening of candidategenes/sequences related to insect's survivability, flight, orreproduction and ultimately affect the vectoring potential of insectvector in developing transgenic citrus. Thus CTV-based silencing vectorwould hasten the process of selecting right candidate sequences forstable transformation. On the other hand, CTV-based silencing vectorcould be used as an interim solution in mitigating the HLB diseasemanifestation at present in the field. The species specificity is thecritical issue that needs to be addressed before using RNAi-based pestcontrol measures in the field. But RNAi technology has the potential toaddress this problem by producing sequence specific and species specificRNAi pesticide (Whyard et al., 2009).

5. Conclusions

Three RNA silencing suppressors of CTV do not prevent CTV from inducinggene silencing in Citrus and N. benthamiana transgenic line 16c.CTV-based plant-mediated RNAi induces gene silencing in phloem-sapsucking insect D. citri, which vectors bacterial disease HLB. ThusCTV-based RNAi vector could be a valuable tool for fast-track screeningcandidate sequences in developing transgenic citrus against citrus pestand diseases. Because of the slow and difficult transgenic methodologyin citrus, CTV-RNAi vector could be an interim solution in mitigatingthe spread of HLB disease in the field.

Genes Related to Example 9:

(a) tGFP (SEQ ID NO. 83) GCTAGCAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGGTGATGTTAATGGGCACAAATTTTCTGTCAGTGGAGAGGGTGAAGGTGATGCTACATACGGAAAGCTTACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCATGGCCAACACTTGTCACTACTTTCTCTTATGGTGTTCAATGCTTTTCCCGTTATCCGGATCATATGAAACGGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAAAGAACTATATTTTTCAAAGATGACGGGAACTACAAGACGCGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTTAATCGTATCGAGTTAAAAGGTATTGATTTTAAAGAAGATGGAAACATTCTCGGACACAAACTC GAGTACAACTATAACTC(b) tPDS (SEQ ID NO. 84) AGCCTTTGCTTCAGCGTTTCTGAAAGTGCTTTCAACTTGCGATATGGTTTCCGAGATAGTGAACCGATGGGTCAGAGCCTGAAAATTCGAGTTAAAACGAGGACAAGGAAGGGTTTCTGTCCTTCGAAGGCGGTTTGTGTGGACTACCCAAGACCAGATATTGATAATACATCTAATTTCTTGGAAGCTGCTTACTTATCTTCGTCATTTCGTACTTCTCCTCGTCCTTCTAAGCCGTTGAAAGTTGTAATTGCTGGTGCAGGTTTGGCTGGTTTATCAACTGCAAAATATTTGGCAGATGCAGGCCACAAGCCTTTGTTACTGGAAGCAAGAGATGTTCTAGGTGGAAAGATAGCTGCCTGGAAAGATGGGGACG GGAACTGGTAGAGAC (c) tAwd(SEQ ID NO. 85) GCCGAACCCAAGGAAAGAACTTTTCTCATGATCAAGCCCGATGGCGTTCAAAGAGGACTTGTGGGAAACATCATCAAACGCTTTGAAGACAAAGGCTTCAAATTGGTGGCCATGAAATTCGTTTGGCCATCCGAAGAACTTCTGAAGCAACACTACTCAGATTTGGCCACCAAACCTTTCTTCCCTGGTCTTGTCAAATACATGTCATCTGGACCTGTTGTTCCTATGGTGTGGGAAGGATTGAACATTGTCAAAACTGGACGTGTGATGCTTGGAGCCACCAACCCTGCTGACTCTGCCCCAGGAACTGTCAGAGGAGACCTCTGCATCCAAGTTGGAAGAAACATCATGCATGGATCAGACTCTGTTGAATCTGCAAAGAAAGAAATTGCCTTATGGTTCACTGAGAAAGAAGTCATTGGATGGACAAATGCCAGTGAATCCTGGATCTATGAATAA

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While various disclosed embodiments have been described above, it shouldbe understood that they have been presented by way of example only, andnot limitation. Numerous changes to the subject matter disclosed hereincan be made in accordance with this Disclosure without departing fromthe spirit or scope of this Disclosure. In addition, while a particularfeature may have been disclosed with respect to only one of severalimplementations, such feature may be combined with one or more otherfeatures of the other implementations as may be desired and advantageousfor any given or particular application.

Thus, the breadth and scope of the subject matter provided in thisDisclosure should not be limited by any of the above explicitlydescribed embodiments. Rather, the scope of this Disclosure should bedefined in accordance with the following claims and their equivalents.

The terminology used herein is for the purpose of describing particularembodiments only and is not intended to be limiting. As used herein, thesingular forms “a,” “an,” and “the” are intended to include the pluralforms as well, unless the context clearly indicates otherwise.Furthermore, to the extent that the terms “including,” “includes,”“having,” “has,” “with,” or variants thereof are used in either thedetailed description and/or the claims, such terms are intended to beinclusive in a manner similar to the term “comprising.”

Unless otherwise defined, all terms (including technical and scientificterms) used herein have the same meaning as commonly understood by oneof ordinary skill in the art to which embodiments belong. It will befurther understood that terms, such as those defined in commonly useddictionaries, should be interpreted as having a meaning that isconsistent with their meaning in the context of the relevant art andwill not be interpreted in an idealized or overly formal sense unlessexpressly so defined herein.

The teachings of any patents, patent applications, technical orscientific articles or other references are incorporated herein in theirentirety to the extent not inconsistent with the teachings herein.

What is claimed is:
 1. A method of infecting a tree with a heterologousgene, said method comprising transfecting at least one cell of said treewith a Citrus tristeza virus (CTV) viral vector engineered to compriseat least one gene cassette comprising a heterologous nucleic acid, theCTV viral vector engineered such that the gene cassette is positioned 3′behind the p23 gene.
 2. The method of claim 1, wherein said heterologousnucleic acid encodes an RNA interfering molecule.
 3. The method of claim2, wherein said RNA interfering molecule targets a nucleic acid of aplant pathogen or a biological vector.
 4. The method of claim 3 whereinthe RNA interfering molecule targets D. citri Awd.